A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

abisolid - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
 
AbortLoadIndexPageController - Class in net.sourceforge.solexatools.webapp.controller
AbortLoadIndexPageController class.
AbortLoadIndexPageController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AbortLoadIndexPageController
Constructor for AbortLoadIndexPageController.
abortTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
abortTransaction.
abortTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
abortTransaction.
abortTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
abortTransaction.
abortTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
abortTransaction.
abortTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
abortTransaction.
AboutResource - Class in com.github.seqware.queryengine.system.rest.resources
Describes the version, back-end, and provides other useful information about the current back-end.
AboutResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.AboutResource
 
AboutResource.BagOfVersionInfo - Class in com.github.seqware.queryengine.system.rest.resources
 
AbstractInMemorySet<S extends MolSetInterface,T> - Class in com.github.seqware.queryengine.model.impl.inMemory
An in-memory representation of a MolSetInterface.
AbstractInMemorySet() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
Constructor for AbstractInMemorySet.
AbstractJob - Class in net.sourceforge.seqware.pipeline.workflowV2.model
 
AbstractJob(String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
for bash Job
AbstractJob(String, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
for Java/Perl/JavaModule job
AbstractMolSet<S extends MolSetInterface> - Class in com.github.seqware.queryengine.model.impl
Implements TTL behaviour for sets
AbstractMolSet() - Constructor for class com.github.seqware.queryengine.model.impl.AbstractMolSet
Constructor for AbstractMolSet.
AbstractWorkflowDataModel - Class in net.sourceforge.seqware.pipeline.workflowV2
 
AbstractWorkflowDataModel() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
AbstractWorkflowEngine - Class in net.sourceforge.seqware.pipeline.workflowV2
 
AbstractWorkflowEngine() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowEngine
 
abundancemeasurement - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
 
accept(Representation) - Method in class net.sourceforge.seqware.queryengine.webservice.view.WorkflowResource
accept.
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
 
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
ACCESSION_ONLY - Static variable in class com.github.seqware.queryengine.system.importers.OBOImporter
Determines whether we use "acccession-only" tags.
accessKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
accessKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
accessKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
ACL - Class in com.github.seqware.queryengine.model.interfaces
Access control list that determines permissions and access rights to features and feature sets.
ACL.Builder - Class in com.github.seqware.queryengine.model.interfaces
 
ACL.Builder() - Constructor for class com.github.seqware.queryengine.model.interfaces.ACL.Builder
 
ACL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
ACLable - Interface in com.github.seqware.queryengine.model.interfaces
Interface for object under access control.
action - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS
 
actions - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
Adag - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object
Adag object match to the element, which is a root element in a dax.
Adag(AbstractWorkflowDataModel) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Adag
 
adapterspec - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
 
adaptor - Variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
 
add(Feature) - Method in class com.github.seqware.queryengine.model.FeatureSet
Add one element to the set
add(Collection<Feature>) - Method in class com.github.seqware.queryengine.model.FeatureSet
Add numerous elements from within a set
add(Feature) - Method in class com.github.seqware.queryengine.model.impl.FeatureList
add.
add(T) - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
Add one element to the set
add(Collection<T>) - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
Add numerous elements from within a set
add(T...) - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
Add an array of elements
add(Feature) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
Add one element to the set
add(Feature...) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
Add an array of elements
add(Collection<Feature>) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
Add numerous elements from within a set
add(Tag) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
Add one element to the set
add(Collection<Tag>) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
Add numerous elements from within a set
add(Tag...) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
Add an array of elements
add(Feature) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
Add one element to the set
add(Feature...) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
Add an array of elements
add(Collection<Feature>) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
Add numerous elements from within a set
add(T) - Method in interface com.github.seqware.queryengine.model.interfaces.MolSetInterface
Add one element to the set
add(Collection<T>) - Method in interface com.github.seqware.queryengine.model.interfaces.MolSetInterface
Add numerous elements from within a set
add(T...) - Method in interface com.github.seqware.queryengine.model.interfaces.MolSetInterface
Add an array of elements
add(Integer, FileAttribute) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService
add.
add(Integer, FileAttribute) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl
add.
add(FileAttribute) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO
add.
add(FileAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
add.
add(WorkflowAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
add.
add(WorkflowRunAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
add.
add(WorkflowAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
add.
add(WorkflowRunAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
add.
add(Experiment) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentList
add.
add(File) - Method in class net.sourceforge.seqware.common.model.lists.FileList
add.
add(IUS) - Method in class net.sourceforge.seqware.common.model.lists.IUSList
add.
add(Lane) - Method in class net.sourceforge.seqware.common.model.lists.LaneList
add.
add(LibrarySelection) - Method in class net.sourceforge.seqware.common.model.lists.LibrarySelectionList
add.
add(LibrarySource) - Method in class net.sourceforge.seqware.common.model.lists.LibrarySourceList
add.
add(LibraryStrategy) - Method in class net.sourceforge.seqware.common.model.lists.LibraryStrategyList
add.
add(Organism) - Method in class net.sourceforge.seqware.common.model.lists.OrganismList
add.
add(Platform) - Method in class net.sourceforge.seqware.common.model.lists.PlatformList
add.
add(Processing) - Method in class net.sourceforge.seqware.common.model.lists.ProcessingList
add.
add(ReturnValue) - Method in class net.sourceforge.seqware.common.model.lists.ReturnValueList
add.
add(Sample) - Method in class net.sourceforge.seqware.common.model.lists.SampleList
add.
add(SequencerRun) - Method in class net.sourceforge.seqware.common.model.lists.SequencerRunList
add.
add(Study) - Method in class net.sourceforge.seqware.common.model.lists.StudyList
add.
add(StudyType) - Method in class net.sourceforge.seqware.common.model.lists.StudyTypeList
add.
add(Workflow) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowList
add.
add(WorkflowParam) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamList
add.
add(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList
add.
add(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList
add.
add(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2
add.
add(String, String) - Method in class net.sourceforge.seqware.pipeline.runner.RunnerParams
add.
add - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
 
add_empty_processing_event(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
add_empty_processing_event.
add_empty_processing_event(int[]) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
add_empty_processing_event.
add_empty_processing_event(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
add_empty_processing_event.
add_empty_processing_event(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
add_empty_processing_event.
add_empty_processing_event_by_parent_accession(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
add_empty_processing_event_by_parent_accession.
add_empty_processing_event_by_parent_accession(int[]) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
add_empty_processing_event_by_parent_accession.
add_empty_processing_event_by_parent_accession(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
add_empty_processing_event_by_parent_accession.
add_empty_processing_event_by_parent_accession(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
add_empty_processing_event_by_parent_accession.
add_task_group(int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
add_task_group.
add_task_group(int[], int[], String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
add_task_group.
add_task_group(int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
add_task_group.
add_task_group(int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
add_task_group.
add_workflow_run(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
add_workflow_run.
add_workflow_run(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
add_workflow_run.
add_workflow_run(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
add_workflow_run.
add_workflow_run(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
add_workflow_run.
add_workflow_run_ancestor(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
add_workflow_run_ancestor.
add_workflow_run_ancestor(int, int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
add_workflow_run_ancestor.
add_workflow_run_ancestor(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
add_workflow_run_ancestor.
add_workflow_run_ancestor(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
add_workflow_run_ancestor.
addACL(ACL) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
addACL.
addAllFeatures(Iterable<? extends QueryEngine.FeaturePB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
addAllFeatures(Iterable<? extends QESupporting.FSGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
addAllFeatureSetIDs(Iterable<? extends QESupporting.SGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
addAllGrps(Iterable<? extends QESupporting.SGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
addAllPluginRunIDs(Iterable<? extends QESupporting.SGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
addAllReferenceIDs(Iterable<? extends QESupporting.SGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
addAllRights(Iterable<? extends Boolean>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
addAllTags(Iterable<? extends QESupporting.TagPB>) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
addAllTags(Iterable<? extends QESupporting.TagPB>) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
addAllTagSpecIDs(Iterable<? extends QESupporting.SGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
addAllUsers(Iterable<? extends QESupporting.SGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
addAnalysisPlugin(AnalysisPlugin) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
addAnalysisPlugin.
addAnalysisSet(AnalysisSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
addAnalysisSet.
addArgument(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
 
addArgument(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
addArgument.
addArgumentPair(String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
addArgumentPair.
addAttribute(AttributeDto) - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributeResource
addAttribute.
addAttribute(AttributeDto) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource
addAttribute.
addDirectory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
create a user defined directory before all jobs started
addElement(String, Atom) - Method in class com.github.seqware.queryengine.system.rest.resources.GenericMutableSetResource
Create a totally new element inside the set given a specification without an associated ID.
addExperiment(Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
addExperiment.
addExperiment(Integer, Integer, String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
addExperiment.
addExperiment(Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
addExperiment.
addExperiment(Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
addExperiment.
addExperiment() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
addFeatures(QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
addFeatures(int, QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
addFeatures(QueryEngine.FeaturePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
addFeatures(int, QueryEngine.FeaturePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
addFeatures(QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
addFeatures(int, QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
addFeatures(QESupporting.FSGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
addFeatures(int, QESupporting.FSGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
addFeaturesBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
addFeaturesBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
addFeaturesBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
addFeaturesBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
addFeatureSet(FeatureSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
addFeatureSet.
addFeatureSetIDs(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
addFeatureSetIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
addFeatureSetIDs(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
addFeatureSetIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
addFeatureSetIDsBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
addFeatureSetIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
addFile(SqwFile) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
add a job specific file for provision
addFile(SqwFile) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
add a job specific file
addGroup(Group) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
addGroup.
addGrps(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
addGrps(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
addGrps(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
addGrps(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
addGrpsBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
addGrpsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
addIUS(Integer, Integer, String, String, String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
addIUS(Integer, Integer, String, String, String, boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
addSample.
addIUS(Integer, Integer, String, String, String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
addIUS(Integer, Integer, String, String, String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
addIUS() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
addJobs(AbstractJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
add job to the workflow
addLane(Integer, Integer, Integer, Integer, Integer, String, String, String, boolean, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
addLane(Integer, Integer, Integer, Integer, Integer, String, String, String, boolean, Integer) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
addSample.
addLane(Integer, Integer, Integer, Integer, Integer, String, String, String, boolean, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
addLane(Integer, Integer, Integer, Integer, Integer, String, String, String, boolean, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
addLane() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
addParent(OozieJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
addParent(PegasusJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
addParent(AbstractJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
add a parent
addParent(Job) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
addParent(Job) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
add job's parent
addParentAccessionFile(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
addParentAccessionFile(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
addPluginRunIDs(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
addPluginRunIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
addPluginRunIDs(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
addPluginRunIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
addPluginRunIDsBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
addPluginRunIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
addProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.Lane
addProcessing.
addProcessings(IUS) - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
addProcessings.
addReference(Reference) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
addReference.
addReferenceIDs(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
addReferenceIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
addReferenceIDs(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
addReferenceIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
addReferenceIDsBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
addReferenceIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
addReferenceSet(ReferenceSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
addReferenceSet.
addRequirement(Requirement) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
addRights(boolean) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
addRow(Flexigrid.Cells) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
addRow.
addSample(Integer, Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
addSample.
addSample(Integer, Integer, Integer, String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
addSample.
addSample(Integer, Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
addSample.
addSample(Integer, Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
addSample.
addSample() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
addSequencerRun(Integer, String, String, boolean, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
addSequencerRun(Integer, String, String, boolean, boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
addSample.
addSequencerRun(Integer, String, String, boolean, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
addSequencerRun(Integer, String, String, boolean, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
FIXME: there are problems with setting accession when I should set ID
addSequencerRun() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
addSet(Atom) - Method in class com.github.seqware.queryengine.system.rest.resources.GenericSetResource
Create a totally new object given a specification without an associated ID.
addStudy(String, String, String, StudyType, String, String, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
addStudy.
addStudy(String, String, String, StudyType, String, String, Integer) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
addStudy.
addStudy(String, String, String, StudyType, String, String, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
addStudy.
addStudy(String, String, String, StudyType, String, String, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
addStudy.
addStudy() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
addTag(String, String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
addTag.
addTag(String, String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
addTag.
addTags(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
addTags(int, QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
addTags(QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
addTags(int, QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
addTags(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
addTags(int, QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
addTags(QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
addTags(int, QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
addTags(Model, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
addTags.
addTags(Model, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
addTags.
addTagsBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
addTagsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
addTagsBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
addTagsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
addTagSet(TagSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
addTagSet.
addTagSpecIDs(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
addTagSpecIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
addTagSpecIDs(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
addTagSpecIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
addTagSpecIDsBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
addTagSpecIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
addTest(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
add a test command for the workflow
addUser(User) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
addUser.
addUsers(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
addUsers(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
addUsers(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
addUsers(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
addUsersBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
addUsersBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
addUserToGroup(User, Group) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
addUserToGroup.
addWorkflow(String, String, String, String, String, String, String, boolean, String, boolean, String, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
addWorkflow.
addWorkflow(String, String, String, String, String, String, String, boolean, String, boolean, String, String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
addWorkflow.
addWorkflow(String, String, String, String, String, String, String, boolean, String, boolean, String, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
addWorkflow.
addWorkflow(String, String, String, String, String, String, String, boolean, String, boolean, String, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
addWorkflow.
addWorkflowRun(String, String, String) - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
addWorkflowRunParam(int, String, String, String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
addWorkflowRunParam.
ADHOC_TAGSETS_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
Constant ADHOC_TAGSETS_PARAM='a'
adhoctagset - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
algorithm - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
algorithmName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
alias - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
alias - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
alias - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
alias - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
 
alias - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
 
alias - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
aligned(String) - Static method in class net.sourceforge.seqware.common.util.TabExpansionUtil
Produce aligned output that lines up properly in the terminal
AlignmentQualityReportDecider - Class in net.sourceforge.seqware.pipeline.deciders
FIXME: this extends the plugin but really it should be a decider subclass.
AlignmentQualityReportDecider() - Constructor for class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider
 
AnalisysBulkDownloadListController - Class in net.sourceforge.solexatools.webapp.controller
AnalisysBulkDownloadListController class.
AnalisysBulkDownloadListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController
Constructor for AnalisysBulkDownloadListController.
AnalisysBulkDownloadListDetailsController - Class in net.sourceforge.solexatools.webapp.controller
AnalisysBulkDownloadListDetailsController class.
AnalisysBulkDownloadListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
Constructor for AnalisysBulkDownloadListDetailsController.
AnalisysEventController - Class in net.sourceforge.solexatools.webapp.controller
StudyController
AnalisysEventController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
Constructor for AnalisysEventController.
AnalisysEventController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
Constructor for AnalisysEventController.
AnalisysListController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
AnalisysListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysListController
Constructor for AnalisysListController.
AnalisysListDetailsController - Class in net.sourceforge.solexatools.webapp.controller
AnalisysListDetailsController class.
AnalisysListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
Constructor for AnalisysListDetailsController.
AnalisysRunningListDetailsController - Class in net.sourceforge.solexatools.webapp.controller
AnalisysRunningListDetailsController class.
AnalisysRunningListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
Constructor for AnalisysRunningListDetailsController.
AnalisysTableController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
AnalisysTableController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysTableController
Constructor for AnalisysListController.
AnalisysTableControllerDetails - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
AnalisysTableControllerDetails() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails
Constructor for AnalisysListController.
analysis - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisSet
 
ANALYSIS_VIEW - Static variable in class net.sourceforge.solexatools.util.Constant
Constant ANALYSIS_VIEW="redirect:/myAnalisysList.htm"
analysisattribute - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES
 
analysisattributes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
analysisCenter - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
analysisfiles - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
analysislink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS
 
analysislinks - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
AnalysisSet - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisSet() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisSet
 
AnalysisType - Class in net.sourceforge.seqware.queryengine.webservice.model
A SRA analysis object captures secondary analysis results from a short read dataset.
AnalysisType() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
analysistype - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
AnalysisType.ANALYSISATTRIBUTES - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISATTRIBUTES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES
 
AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
 
AnalysisType.ANALYSISFILES - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISFILES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES
 
AnalysisType.ANALYSISFILES.FILE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISFILES.FILE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE
 
AnalysisType.ANALYSISLINKS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISLINKS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS
 
AnalysisType.ANALYSISLINKS.ANALYSISLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISLINKS.ANALYSISLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
 
AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
 
AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
 
AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
 
AnalysisType.ANALYSISTYPE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.ANALYSISTYPE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
 
AnalysisType.PARENT - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.PARENT() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
 
AnalysisType.PARENT.EXPERIMENTREF - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.PARENT.EXPERIMENTREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF
 
AnalysisType.PARENT.RUNREF - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.PARENT.RUNREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF
 
AnalysisType.PARENT.SAMPLEPOOLREF - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.PARENT.SAMPLEPOOLREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF
 
AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
 
AnalysisType.PARENT.SAMPLEREF - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.PARENT.SAMPLEREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF
 
AnalysisType.PARENT.STUDYREF - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
AnalysisType.PARENT.STUDYREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF
 
AND - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant AND=4
AND - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant AND=4
annotateExperiment(int, ExperimentAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
annotateExperiment.
annotateExperiment(int, Set<ExperimentAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
annotateExperiment.
annotateExperiment(int, ExperimentAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
annotateExperiment.
annotateExperiment(int, Set<ExperimentAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
annotateExperiment.
annotateExperiment(int, ExperimentAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
annotateExperiment.
annotateExperiment(int, Set<ExperimentAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
annotateExperiment.
annotateExperiment(int, ExperimentAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
annotateExperiment.
annotateExperiment(int, Set<ExperimentAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
annotateExperiment.
annotateIUS(int, IUSAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
annotateIUS.
annotateIUS(int, Set<IUSAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
annotateIUS.
annotateIUS(int, IUSAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
annotateIUS.
annotateIUS(int, Set<IUSAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
annotateIUS.
annotateIUS(int, IUSAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
annotateIUS.
annotateIUS(int, Set<IUSAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
annotateIUS.
annotateIUS(int, IUSAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
annotateIUS.
annotateIUS(int, Set<IUSAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
annotateIUS.
annotateLane(int, LaneAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
annotateLane.
annotateLane(int, Set<LaneAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
annotateLane.
annotateLane(int, LaneAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
annotateLane.
annotateLane(int, Set<LaneAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
annotateLane.
annotateLane(int, LaneAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
annotateLane.
annotateLane(int, Set<LaneAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
annotateLane.
annotateLane(int, LaneAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
annotateLane.
annotateLane(int, Set<LaneAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
annotateLane.
annotateProcessing(int, ProcessingAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
annotateProcessing.
annotateProcessing(int, Set<ProcessingAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
annotateProcessing.
annotateProcessing(int, ProcessingAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
annotateProcessing.
annotateProcessing(int, Set<ProcessingAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
annotateProcessing.
annotateProcessing(int, ProcessingAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
annotateProcessing.
annotateProcessing(int, Set<ProcessingAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
annotateProcessing.
annotateProcessing(int, ProcessingAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
annotateProcessing.
annotateProcessing(int, Set<ProcessingAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
annotateProcessing.
annotateSample(int, SampleAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
annotateSample.
annotateSample(int, Set<SampleAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
annotateSample.
annotateSample(int, SampleAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
annotateSample.
annotateSample(int, Set<SampleAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
annotateSample.
annotateSample(int, SampleAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
annotateSample.
annotateSample(int, Set<SampleAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
annotateSample.
annotateSample(int, SampleAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
annotateSample.
annotateSample(int, Set<SampleAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
annotateSample.
annotateSequencerRun(int, SequencerRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
annotateSequencerRun.
annotateSequencerRun(int, Set<SequencerRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
annotateSequencerRun.
annotateSequencerRun(int, SequencerRunAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
annotateSequencerRun.
annotateSequencerRun(int, Set<SequencerRunAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
annotateSequencerRun.
annotateSequencerRun(int, SequencerRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
annotateSequencerRun.
annotateSequencerRun(int, Set<SequencerRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
annotateSequencerRun.
annotateSequencerRun(int, SequencerRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
annotateSequencerRun.
annotateSequencerRun(int, Set<SequencerRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
annotateSequencerRun.
annotateStudy(int, StudyAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
annotateStudy.
annotateStudy(int, Set<StudyAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
annotateStudy.
annotateStudy(int, StudyAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
annotateStudy.
annotateStudy(int, Set<StudyAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
annotateStudy.
annotateStudy(int, StudyAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
annotateStudy.
annotateStudy(int, Set<StudyAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
annotateStudy.
annotateStudy(int, StudyAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
annotateStudy.
annotateStudy(int, Set<StudyAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
annotateStudy.
AnnotateVariantsWithContigAndZygosity - Class in net.sourceforge.seqware.queryengine.tools.annotators
AnnotateVariantsWithContigAndZygosity class.
AnnotateVariantsWithContigAndZygosity() - Constructor for class net.sourceforge.seqware.queryengine.tools.annotators.AnnotateVariantsWithContigAndZygosity
 
annotateWorkflow(int, WorkflowAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
annotateWorkflow.
annotateWorkflow(int, Set<WorkflowAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
annotateWorkflow.
annotateWorkflow(int, WorkflowAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
annotateWorkflow.
annotateWorkflow(int, Set<WorkflowAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
annotateWorkflow.
annotateWorkflow(int, WorkflowAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
annotateWorkflow.
annotateWorkflow(int, Set<WorkflowAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
annotateWorkflow.
annotateWorkflow(int, WorkflowAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
annotateWorkflow.
annotateWorkflow(int, Set<WorkflowAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
annotateWorkflow.
annotateWorkflowRun(int, WorkflowRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
annotateWorkflowRun.
annotateWorkflowRun(int, Set<WorkflowRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
annotateWorkflowRun.
annotateWorkflowRun(int, WorkflowRunAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
annotateWorkflowRun.
annotateWorkflowRun(int, Set<WorkflowRunAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
annotateWorkflowRun.
annotateWorkflowRun(int, WorkflowRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
annotateWorkflowRun.
annotateWorkflowRun(int, Set<WorkflowRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
annotateWorkflowRun.
annotateWorkflowRun(int, WorkflowRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
annotateWorkflowRun.
annotateWorkflowRun(int, Set<WorkflowRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
annotateWorkflowRun.
annotationAwareAspectJAutoProxyCreator() - Method in class net.sourceforge.seqware.pipeline.runner.Runner2.ModuleConfig
 
anonymizedname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
 
ApacheSerialization - Class in com.github.seqware.queryengine.impl
ApacheSerialization class.
ApacheSerialization() - Constructor for class com.github.seqware.queryengine.impl.ApacheSerialization
 
ApiException - Exception in com.github.seqware.queryengine.system.rest.exception
Based on swagger's Sample App
ApiException(int, String) - Constructor for exception com.github.seqware.queryengine.system.rest.exception.ApiException
 
APP - Static variable in interface net.sourceforge.seqware.pipeline.runner.RunnerParams.Bean
 
appID - Variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
 
appID - Static variable in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
 
Argument - Class in net.sourceforge.seqware.pipeline.workflowV2.model
Argument class.
Argument(String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
Constructor for Argument.
asDto(SampleSearch) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
asDto.
asDto(Attribute) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
asDto.
asDto(Registration) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
asDto.
asDto(Sample) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
asDto.
asDto(IUS) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
asDto.
asDto(File) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
asDto.
aSet - Variable in class com.github.seqware.queryengine.model.FeatureSet.Builder
 
aSet - Variable in class com.github.seqware.queryengine.model.Group.Builder
 
aSet - Variable in class com.github.seqware.queryengine.model.Plugin.Builder
 
aSet - Variable in class com.github.seqware.queryengine.model.ReferenceSet.Builder
 
aSet - Variable in class com.github.seqware.queryengine.model.TagSet.Builder
 
associate_processing_event_with_parents_and_child(int, int[], int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
associate_processing_event_with_parents_and_child.
associate_processing_event_with_parents_and_child(int, int[], int[]) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
associate_processing_event_with_parents_and_child.
associate_processing_event_with_parents_and_child(int, int[], int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
associate_processing_event_with_parents_and_child.
associate_processing_event_with_parents_and_child(int, int[], int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
associate_processing_event_with_parents_and_child.
associateTag(Tag) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
associate new tag to a subject with a null value and a null predicate
associateTag(Tag) - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable
associate new tag to a subject with a null value and a null predicate
associateTag(Tag) - Method in class com.github.seqware.queryengine.model.Tag
associate new tag to a subject with a null value and a null predicate
atDto(Organism) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
atDto.
Atom<T extends Atom> - Interface in com.github.seqware.queryengine.model
Implements core functionality that is shared by all classes that require tags.
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
AtomImpl<T extends Atom> - Class in com.github.seqware.queryengine.model.impl
Implements core functionality that is shared by all classes that require tags.
AtomImpl() - Constructor for class com.github.seqware.queryengine.model.impl.AtomImpl
Constructor for AtomImpl.
AtomImpl.TagValueIterable - Class in com.github.seqware.queryengine.model.impl
 
AtomImpl.TagValueIterable(Map<String, Map<String, Tag>>) - Constructor for class com.github.seqware.queryengine.model.impl.AtomImpl.TagValueIterable
 
AtomImpl.TagValueIterator - Class in com.github.seqware.queryengine.model.impl
 
AtomImpl.TagValueIterator(Map<String, Map<String, Tag>>) - Constructor for class com.github.seqware.queryengine.model.impl.AtomImpl.TagValueIterator
 
atomStateChange(Atom, CreateUpdateManager.State) - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Called by Atoms when they need to change state (for example, to notify that they have become a dirty new version)
atomStateChange(Atom, CreateUpdateManager.State) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Called by Atoms when they need to change state (for example, to notify that they have become a dirty new version)
Attribute - Interface in net.sourceforge.seqware.common.model
Attribute interface.
attribute - Variable in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
 
AttributeAnnotator - Class in net.sourceforge.seqware.pipeline.plugins
AttributeAnnotator class.
AttributeAnnotator() - Constructor for class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator
Constructor for AttributeAnnotator.
AttributeDto - Class in net.sourceforge.seqware.webservice.dto
 
AttributeDto() - Constructor for class net.sourceforge.seqware.webservice.dto.AttributeDto
 
attributes - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
authenticate() - Method in class net.sourceforge.seqware.webservice.resources.BasicResource
authenticate.
authenticate(String) - Method in class net.sourceforge.seqware.webservice.resources.BasicRestlet
authenticate.
Authentication - Class in net.sourceforge.solexatools.authentication
Abstract Authentication class.
Authentication() - Constructor for class net.sourceforge.solexatools.authentication.Authentication
 
AUTOFLUSH - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
Constant AUTOFLUSH=false
available - Variable in class com.github.seqware.queryengine.system.importers.Importer
 
available - Variable in class net.sourceforge.seqware.queryengine.tools.importers.Importer
 

B

BackEndInterface - Interface in com.github.seqware.queryengine.backInterfaces
A singular interface that needs to be implemented in order for a back-end developer to add support for a particular new back-end.
BackendPool - Class in net.sourceforge.seqware.queryengine.webservice.model
BackendPool class.
BackendPool() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.BackendPool
 
backendRequest() - Method in class com.github.seqware.queryengine.system.rest.resources.AboutResource
List of debug information
BadFile - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode
Constant BadFile=3
BadModule - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode
Constant BadModule=4
BadParameter - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode
Constant BadParameter=2
BadRunnerParams - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode
Constant BadRunnerParams=5
barcodeSeqence - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
 
BASE_URI - Static variable in class com.github.seqware.queryengine.system.rest.QueryEngineService
 
BaseBuilder<S,T extends BaseBuilder> - Class in com.github.seqware.queryengine.model.interfaces
Builders are used to construct Atom.
BaseBuilder() - Constructor for class com.github.seqware.queryengine.model.interfaces.BaseBuilder
 
basecaller - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS
 
basecalls - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING
 
basecoord - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
 
basedir - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
baseQualities - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
BashJob - Class in net.sourceforge.seqware.pipeline.workflowV2.model
 
BashJob(String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.BashJob
 
BasicDecider - Class in net.sourceforge.seqware.pipeline.deciders
 
BasicDecider() - Constructor for class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
BasicDecider.FILE_STATUS - Enum in net.sourceforge.seqware.pipeline.deciders
These file statuses reflect the discussion at https://wiki.oicr.on.ca/display/SEQWARE/2013/01/15/Jan+15%2C+2013%3A+Problematic+Basic+Decider+Logic
BasicDecider.PREVIOUS_RUN_STATUS - Enum in net.sourceforge.seqware.pipeline.deciders
We care about three types of status, an outright fail, other (pending, running, submitted, etc.), and completed
BasicResource - Class in net.sourceforge.seqware.webservice.resources
See https://sourceforge.net/apps/mediawiki/seqware/index.php?title=How_to_extend_the_web_service#Basic_Resource
BasicResource() - Constructor for class net.sourceforge.seqware.webservice.resources.BasicResource
Constructor for BasicResource.
BasicRestlet - Class in net.sourceforge.seqware.webservice.resources
See https://sourceforge.net/apps/mediawiki/seqware/index.php?title=How_to_extend_the_web_service#Basic_Resource
BasicRestlet(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.BasicRestlet
Constructor for BasicRestlet.
BasicWorkflow - Class in net.sourceforge.seqware.pipeline.workflow
Abstract BasicWorkflow class.
BasicWorkflow(Metadata, Map<String, String>) - Constructor for class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
Constructor for BasicWorkflow.
BasicWorkflow.Job - Enum in net.sourceforge.seqware.pipeline.workflow
 
BATCH_SIZE - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
Constant BATCH_SIZE=100000
batch_size - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
BATCH_SIZE_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
Constant BATCH_SIZE_PARAM='b'
BatchMetadataInjection - Class in net.sourceforge.seqware.pipeline.plugins
BatchImport class.
BatchMetadataInjection() - Constructor for class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection
Constructor for AttributeAnnotator.
BatchMetadataInjection.Header - Class in net.sourceforge.seqware.pipeline.plugins
 
BatchMetadataInjection.Header() - Constructor for class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.Header
 
BatchMetadataInjection.RunInfo - Class in net.sourceforge.seqware.pipeline.plugins
 
BatchMetadataInjection.RunInfo() - Constructor for class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.RunInfo
 
BatchMetadataInjection.SampleInfo - Class in net.sourceforge.seqware.pipeline.plugins
 
BatchMetadataInjection.SampleInfo() - Constructor for class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
 
BeanFactory - Class in net.sourceforge.seqware.common.factory
Abstract BeanFactory class.
BeanFactory() - Constructor for class net.sourceforge.seqware.common.factory.BeanFactory
 
BEDExporter - Class in net.sourceforge.seqware.queryengine.tools.exporters
BEDExporter class.
BEDExporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.exporters.BEDExporter
 
BedFeatureImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
BedFeatureImportWorker class.
BedFeatureImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.BedFeatureImportWorker
Constructor for BedFeatureImportWorker.
benchmark() - Method in class com.github.seqware.queryengine.tutorial.Poster
benchmark.
benchmark() - Method in class com.github.seqware.queryengine.tutorial.PosterSGE
benchmark.
BENCHMARKING_BATCH_SIZE - Static variable in class com.github.seqware.queryengine.tutorial.Poster
Constant BENCHMARKING_BATCH_SIZE=20000
BENCHMARKING_BATCH_SIZE - Static variable in class com.github.seqware.queryengine.tutorial.PosterSGE
Constant BENCHMARKING_BATCH_SIZE=20000
BerkeleyDBFactory - Class in net.sourceforge.seqware.queryengine.backend.factory.impl
BerkeleyDBFactory class.
BerkeleyDBFactory() - Constructor for class net.sourceforge.seqware.queryengine.backend.factory.impl.BerkeleyDBFactory
 
BerkeleyDBStore - Class in net.sourceforge.seqware.queryengine.backend.store.impl
BerkeleyDBStore class.
BerkeleyDBStore() - Constructor for class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
 
biMap - Static variable in class com.github.seqware.queryengine.impl.ProtobufSerialization
 
bind(HttpServletRequest, Object) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
bindSessionToThread() - Static method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions
bindSessionToThread.
bindSessionToThread(FlushMode) - Static method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions
bindSessionToThread.
binSize - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
BlobReaderWriter - Class in net.sourceforge.seqware.queryengine.prototypes
BlobReaderWriter class.
BlobReaderWriter() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.BlobReaderWriter
 
blockCount - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
blockSizes - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
blockStarts - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
Bootstrap - Class in com.github.seqware.queryengine.system.rest
Swagger hack to remove format string from their json file locations.
Bootstrap() - Constructor for class com.github.seqware.queryengine.system.rest.Bootstrap
 
BRACKET_CLOSE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant BRACKET_CLOSE=5
BRACKET_CLOSE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant BRACKET_CLOSE=5
BRACKET_OPEN - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant BRACKET_OPEN=6
BRACKET_OPEN - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant BRACKET_OPEN=6
BrianTest - Class in com.github.seqware.queryengine.tutorial
This is a quick and sample application built on top of our API, created during the August 9th Hackathon.
BrianTest(String[]) - Constructor for class com.github.seqware.queryengine.tutorial.BrianTest
Constructor for BrianTest.
brokerName - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
BufferedReaderThread - Class in net.sourceforge.seqware.common.util.iotools
BufferedReaderThread class.
BufferedReaderThread(InputStream) - Constructor for class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
Constructor for BufferedReaderThread.
BUFFERSIZE - Static variable in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController
Constant BUFFERSIZE=500*1024
build() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
build() - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
build() - Method in class com.github.seqware.queryengine.model.FeatureSet.Builder
 
build() - Method in class com.github.seqware.queryengine.model.Group.Builder
 
build(boolean) - Method in class com.github.seqware.queryengine.model.Group.Builder
 
build() - Method in class com.github.seqware.queryengine.model.impl.FeatureList.Builder
 
build() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet.Builder
 
build(boolean) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup.Builder
 
build(boolean) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryPlugin.Builder
 
build() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference.Builder
 
build(boolean) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet.Builder
 
build(boolean) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet.Builder
 
build() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.Builder
 
build() - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder
 
build() - Method in class com.github.seqware.queryengine.model.interfaces.BaseBuilder
Build a Atom
build() - Method in class com.github.seqware.queryengine.model.Plugin.Builder
 
build(boolean) - Method in class com.github.seqware.queryengine.model.Plugin.Builder
 
build() - Method in class com.github.seqware.queryengine.model.PluginRun.Builder
 
build() - Method in class com.github.seqware.queryengine.model.Reference.Builder
 
build() - Method in class com.github.seqware.queryengine.model.ReferenceSet.Builder
 
build(boolean) - Method in class com.github.seqware.queryengine.model.ReferenceSet.Builder
 
build() - Method in class com.github.seqware.queryengine.model.Tag.Builder
 
build() - Method in class com.github.seqware.queryengine.model.TagSet.Builder
 
build(boolean) - Method in class com.github.seqware.queryengine.model.TagSet.Builder
 
build() - Method in class com.github.seqware.queryengine.model.User.Builder
 
Buildable<T extends BaseBuilder> - Interface in com.github.seqware.queryengine.model.interfaces
An interface for the various builders that we will use to construct models for managed objects
buildCommandString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJavaJob
 
buildCommandString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
for overridden by a specific job type
buildCommandString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusPerlJob
 
buildCommandString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob
 
buildDirectory(File) - Static method in class net.sourceforge.solexatools.util.ZipFileUtil
buildDirectory.
buildFeature() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a feature
buildFeature() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Build a feature
buildFeatureSet() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a featureSet with a reference
buildFeatureSet() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Build a featureSet with a reference
buildFeatureSetInternal() - Method in class com.github.seqware.queryengine.impl.MRHBaseModelManager
buildFeatureSetInternal.
buildFeatureSetInternal() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
buildFeatureSetInternal.
buildGroup() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a group
buildGroup() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Build a group
buildMetadataString(Element) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
buildMetadataString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
buildPlugin() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a plugin
buildPlugin() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Build a plugin
buildPluginRun() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a new pluginRun
buildPluginRun() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Build a new pluginRun
buildReference() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a Reference with a given name
buildReference() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Build a Reference with a given name
buildReferenceSet() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a new reference set
buildReferenceSet() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Build a new reference set
buildTag() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a Tag
buildTag() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Build a Tag
buildTagSet() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a set of tags
buildTagSet() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Build a set of tags
buildUser() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Build a user
buildUser() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Build a user
buildWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
to be Overridden by the workflow author
buildWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.XmlWorkflowDataModel
 
BulkDownloaderController - Class in net.sourceforge.solexatools.webapp.controller
BulkDownloaderController class.
BulkDownloaderController() - Constructor for class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController
Constructor for BulkDownloaderController.
BulkDownloaderSizeValidatorController - Class in net.sourceforge.solexatools.webapp.controller
BulkDownloaderSizeValidatorController class.
BulkDownloaderSizeValidatorController() - Constructor for class net.sourceforge.solexatools.webapp.controller.BulkDownloaderSizeValidatorController
 
BulkDownloadListController - Class in net.sourceforge.solexatools.webapp.controller
BulkDownloadListController class.
BulkDownloadListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController
Constructor for BulkDownloadListController.
BulkDownloadListDetailsController - Class in net.sourceforge.solexatools.webapp.controller
BulkDownloadListDetailsController class.
BulkDownloadListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
Constructor for BulkDownloadListDetailsController.
BulkProvisionFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities
Purpose: This module takes one or more inputs (S3 URL, HTTP/HTTPS URL, or local file path) and copies the file to the specified output (S3 bucket URL, HTTP/HTTPS URL, or local directory path).
BulkProvisionFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
 
BulkUtil - Class in net.sourceforge.solexatools.util
BulkUtil class.
BulkUtil() - Constructor for class net.sourceforge.solexatools.util.BulkUtil
 
Bundle - Class in net.sourceforge.seqware.pipeline.bundle
This is a utility class that lets you manipulate a workflow bundle.
Bundle() - Constructor for class net.sourceforge.seqware.pipeline.bundle.Bundle
Constructor for Bundle.
Bundle(Metadata, Map<String, String>) - Constructor for class net.sourceforge.seqware.pipeline.bundle.Bundle
Constructor for Bundle.
bundleDir - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
BundleInfo - Class in net.sourceforge.seqware.pipeline.bundle
BundleInfo class.
BundleInfo() - Constructor for class net.sourceforge.seqware.pipeline.bundle.BundleInfo
 
BundleManager - Class in net.sourceforge.seqware.pipeline.plugins
BundleManager class.
BundleManager() - Constructor for class net.sourceforge.seqware.pipeline.plugins.BundleManager
Constructor for BundleManager.
bundleUtil - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
byte2HexString(byte[]) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
byte2HexString.
BYTEA - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
Constant BYTEA=1
BYTEA - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
Constant BYTEA=1
BYTEA - Static variable in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Constant BYTEA=1
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureIO
Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureListIO
Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureSetIO
Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.GroupIO
Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.PluginIO
Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.PluginRunIO
Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in interface com.github.seqware.queryengine.impl.protobufIO.ProtobufTransferInterface
Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.ReferenceIO
Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.ReferenceSetIO
Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagIO
Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagSetIO
Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagSpecIO
Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.UserIO
Convert from protein buffer object in byte array to model.

C

CachedTagResource - Class in net.sourceforge.seqware.queryengine.webservice.view
CachedTagResource class.
CachedTagResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.CachedTagResource
 
calculateTotalTime(Collection<Processing>) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
calculateTotalTime.
calledBase - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
calledBaseCount - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
calledBaseCountForward - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
calledBaseCountReverse - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
callOne - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
callTwo - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
CancelAnalysisWorkflowController - Class in net.sourceforge.solexatools.webapp.controller
CancelAnalysisWorkflowController class.
CancelAnalysisWorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController
Constructor for CancelAnalysisWorkflowController.
CancelBulkDownloaderController - Class in net.sourceforge.solexatools.webapp.controller
CancelBulkDownloaderController class.
CancelBulkDownloaderController() - Constructor for class net.sourceforge.solexatools.webapp.controller.CancelBulkDownloaderController
Constructor for CancelBulkDownloaderController.
CancelInputDownloaderController - Class in net.sourceforge.solexatools.webapp.controller
CancelInputDownloaderController class.
CancelInputDownloaderController() - Constructor for class net.sourceforge.solexatools.webapp.controller.CancelInputDownloaderController
Constructor for CancelInputDownloaderController.
CASCADE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
causedBy(Throwable, Class) - Static method in class net.sourceforge.seqware.common.util.exceptiontools.ExceptionTools
causedBy.
centerName - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
centername - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
 
centerName - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
centerprojectname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
 
cfg - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
ChangeNumberPopupPageController - Class in net.sourceforge.solexatools.webapp.controller
ChangeNumberPopupPageController class.
ChangeNumberPopupPageController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ChangeNumberPopupPageController
Constructor for ChangeNumberPopupPageController.
ChangeWorkflowParamValueController - Class in net.sourceforge.solexatools.webapp.controller
ChangeWorkflowParamValueController class.
ChangeWorkflowParamValueController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController
Constructor for ChangeWorkflowParamValueController.
CHECK - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant CHECK="check"
CHECK - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
Constant CHECK="check"
checkExit(int) - Method in class net.sourceforge.seqware.common.util.NoExitSecurityManager
checkFields(String[]) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
checkFileDetails(ReturnValue, FileMetadata) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
Performs any additional checks on the file before adding it to the list of files to incorporate.
CheckForCycles - Class in net.sourceforge.seqware.common.hibernate
CheckForCycles class.
CheckForCycles() - Constructor for class net.sourceforge.seqware.common.hibernate.CheckForCycles
 
checkFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.interfaces.BaseBuilder
Check a row key
checkOutput(String) - Static method in class com.github.seqware.queryengine.system.Utility
Check whether we can create the output for a particular filename
checkPassword(String) - Method in class com.github.seqware.queryengine.model.User
Check a user's password
checkPermission(Permission) - Method in class net.sourceforge.seqware.common.util.NoExitSecurityManager
checkPermission(Permission, Object) - Method in class net.sourceforge.seqware.common.util.NoExitSecurityManager
checkpoint() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
checkpoint.
checkProcessing(Processing) - Method in class net.sourceforge.seqware.common.hibernate.CheckForCycles
checkProcessing.
checkSample(Sample) - Method in class net.sourceforge.seqware.common.hibernate.CheckForCycles
checkSample.
checkStudy(Integer) - Method in class net.sourceforge.seqware.common.hibernate.CheckForCycles
checkStudy.
checksum - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
 
checksumMethod - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
 
childMaps - Variable in class com.github.seqware.queryengine.model.interfaces.Taggable.NestedLevel
 
children - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
childTags - Variable in class com.github.seqware.queryengine.model.interfaces.Taggable.NestedLevel
 
clean_up() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
clean_up.
clean_up() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
clean_up.
clean_up() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
clean_up.
clean_up() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
clean_up.
clean_up() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
 
clean_up() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider
Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.module.Module
clean_up.
clean_up() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
clean_up.
clean_up() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator
Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection
Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager
Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker
Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner
Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.OozieXML2Dot
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot
 
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter
Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter
Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter
Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
Perform post-task clean-up here.
cleanup(Mapper.Context) - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner.PluginRunnerMapper
 
cleanup() - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
 
cleanup() - Method in interface com.github.seqware.queryengine.plugins.PluginInterface
cleanup.
clear() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clear() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Erase the current set of managed models without saving them to the back-end
clear() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Erase the current set of managed models without saving them to the back-end
clearAcl() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clearCascade() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
clearDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
clearDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
clearDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
clearDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
clearDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
clearEmailAddress() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clearExpiryTime() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
clearFeatures() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
clearFeatures() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
clearFeatureSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
clearFeatureSetIDs() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
clearFirstName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clearFriendlyRowkey() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
clearGrp() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
clearGrps() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clearId() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearLastName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clearLeastSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clearMostSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
clearName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
clearName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
clearName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
clearName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
clearName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
clearOrganism() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
clearParameters() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
clearPassword() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clearPhase() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearPluginRunIDs() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
clearPragma() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
clearPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clearPredicate() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearReferenceID() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
clearReferenceIDs() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
clearRefName() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
clearRights() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
clearRowKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
clearScore() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
clearSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
clearSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
clearSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
clearSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
clearSource() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearStart() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearStop() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearStorage() - Method in class com.github.seqware.queryengine.backInterfaces.StorageInterface
For debugging or testing purposes, this will wipe out all objects in the serialization store
clearStorage() - Method in class com.github.seqware.queryengine.impl.HBaseStorage
For debugging or testing purposes, this will wipe out all objects in the serialization store
clearStorage() - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
For debugging or testing purposes, this will wipe out all objects in the serialization store
clearStorage() - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
For debugging or testing purposes, this will wipe out all objects in the serialization store
clearStrand() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearTags() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
clearTags() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
clearTagSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearTagSpecIDs() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
clearTimestamp() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
clearTombstone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
clearType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clearUser() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
clearUsers() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
clearVBytes() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearVDouble() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearVFloat() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearVInteger() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearVLong() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearVSGIDRef() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clearVString() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
cli2Map(String[], Map<String, String>) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools
Method to getValues all "--key=value" or "--key value" parameters and add them to hashmap
clone() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
clone(Processing) - Static method in class net.sourceforge.seqware.common.model.Processing
clone.
clone() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
clone() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
cloneFromDB(int) - Static method in class net.sourceforge.seqware.common.model.File
cloneFromDB.
cloneFromDB(int) - Static method in class net.sourceforge.seqware.common.model.Processing
cloneFromDB.
cloneFromDB(int) - Static method in class net.sourceforge.seqware.common.model.Registration
cloneFromDB.
cloneFromDB(int) - Static method in class net.sourceforge.seqware.common.model.WorkflowRun
cloneFromDB.
cloneToHibernate(Processing) - Static method in class net.sourceforge.seqware.common.model.Processing
cloneToHibernate.
cloneToHibernate(WorkflowRun) - Static method in class net.sourceforge.seqware.common.model.WorkflowRun
cloneToHibernate.
close() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Convenience method to flush() all entities and clear().
close() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Convenience method to flush() all entities and clear().
close() - Static method in class net.sourceforge.seqware.common.factory.DBAccess
close.
close() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
close.
close() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator
close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator
close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator
close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator
close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator
close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator
close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator
close.
close() - Method in interface net.sourceforge.seqware.queryengine.backend.util.SeqWareIterator
close.
closeBufferWriter() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
closeImpl() - Method in class com.github.seqware.queryengine.util.InMemoryIterator
Closes the database iterator.
closeImpl() - Method in class com.github.seqware.queryengine.util.SeqWareIterator
Closes the database iterator.
closeStorage() - Method in class com.github.seqware.queryengine.backInterfaces.StorageInterface
Some storage types should be explicitly told when shutting down to release resources.
closeStorage() - Static method in class com.github.seqware.queryengine.factory.SWQEFactory
Close the currently operating storage method
closeStorage() - Method in class com.github.seqware.queryengine.impl.HBaseStorage
Some storage types should be explicitly told when shutting down to release resources.
closeStorage() - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
Some storage types should be explicitly told when shutting down to release resources.
closeStorage() - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
Some storage types should be explicitly told when shutting down to release resources.
codingStart - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
codingStop - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
collectProcessingList(int) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDProcessingsResource
collectProcessingList.
collectProcessings(WorkflowRun) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
 
color - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX
 
colormatrix - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
 
colormatrixcode - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
 
com.github.seqware.queryengine - package com.github.seqware.queryengine
The base directory for the SeqWare Query Engine, we only have constants defined here for now.
com.github.seqware.queryengine.backInterfaces - package com.github.seqware.queryengine.backInterfaces
Provides interfaces that are only of interest to users working on the back-end
com.github.seqware.queryengine.dto - package com.github.seqware.queryengine.dto
 
com.github.seqware.queryengine.factory - package com.github.seqware.queryengine.factory
Provides the classes that the RESTful interface will use to construct interfaces that use the back-end without reference to the specific back-end.
com.github.seqware.queryengine.impl - package com.github.seqware.queryengine.impl
Provides the classes that implement the actual back-end for various database (or lack of database) types
com.github.seqware.queryengine.impl.protobufIO - package com.github.seqware.queryengine.impl.protobufIO
This package contains the classes that specifically handle protobuffer serialization to and from the back-end.
com.github.seqware.queryengine.impl.tuplebinderIO - package com.github.seqware.queryengine.impl.tuplebinderIO
This package contains the a couple of experimental classes that would have to be substantially added to in order to add BerkeleyDB serialization support.
com.github.seqware.queryengine.kernel - package com.github.seqware.queryengine.kernel
This package contains supporting classes for Queries.
com.github.seqware.queryengine.kernel.output - package com.github.seqware.queryengine.kernel.output
 
com.github.seqware.queryengine.model - package com.github.seqware.queryengine.model
Provides the classes that the RESTful API will interact with.
com.github.seqware.queryengine.model.impl - package com.github.seqware.queryengine.model.impl
Provides the classes that implement model entities that the RESTful interface will interact with
com.github.seqware.queryengine.model.impl.hbasemrlazy - package com.github.seqware.queryengine.model.impl.hbasemrlazy
Provides classes that 'lazily' allow their members to persist their own membership and use Map/Reduce to determine attributes about themselves.
com.github.seqware.queryengine.model.impl.inMemory - package com.github.seqware.queryengine.model.impl.inMemory
Provides classes that support a simple in-memory implementation of the various model classes.
com.github.seqware.queryengine.model.impl.lazy - package com.github.seqware.queryengine.model.impl.lazy
Provides classes that 'lazily' allow their members to persist their own membership.
com.github.seqware.queryengine.model.interfaces - package com.github.seqware.queryengine.model.interfaces
 
com.github.seqware.queryengine.plugins - package com.github.seqware.queryengine.plugins
Provides the interfaces that an external plugin developer would need to conform to in order for the Query Engine to install and run properly.
com.github.seqware.queryengine.plugins.hbasemr - package com.github.seqware.queryengine.plugins.hbasemr
Provides classes that support and implement hbase implementations of plug-ins.
com.github.seqware.queryengine.plugins.inmemory - package com.github.seqware.queryengine.plugins.inmemory
Provides classes that support and implement in-memory mock-ups for plugins.
com.github.seqware.queryengine.plugins.plugins - package com.github.seqware.queryengine.plugins.plugins
Provides plug-in implementations
com.github.seqware.queryengine.system - package com.github.seqware.queryengine.system
 
com.github.seqware.queryengine.system.exporters - package com.github.seqware.queryengine.system.exporters
Command-line tools for exporting files to external file types.
com.github.seqware.queryengine.system.importers - package com.github.seqware.queryengine.system.importers
Command-line tools for importing files from external file types.
com.github.seqware.queryengine.system.importers.workers - package com.github.seqware.queryengine.system.importers.workers
Multi-threaded workers that handle the actual work for the FeatureImporter when exporting to various external file types.
com.github.seqware.queryengine.system.rest - package com.github.seqware.queryengine.system.rest
 
com.github.seqware.queryengine.system.rest.exception - package com.github.seqware.queryengine.system.rest.exception
 
com.github.seqware.queryengine.system.rest.resources - package com.github.seqware.queryengine.system.rest.resources
 
com.github.seqware.queryengine.tutorial - package com.github.seqware.queryengine.tutorial
Classes for testing and hacking new tools.
com.github.seqware.queryengine.util - package com.github.seqware.queryengine.util
Provides utility classes for accessing this API via the model
com.github.seqware.queryengine.util.obo - package com.github.seqware.queryengine.util.obo
 
Command - Class in net.sourceforge.seqware.pipeline.workflowV2.model
 
Command() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Command
 
commaSeparateMy(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
comment() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
comment.
COMMENT_EOL - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant COMMENT_EOL=7
COMMENT_EOL - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant COMMENT_EOL=7
COMMENT_INLINE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant COMMENT_INLINE=8
COMMENT_INLINE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant COMMENT_INLINE=8
commonname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
 
commonTimestamp - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
compare(ExperimentSpotDesignReadSpec, ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.model.comparator.ExperimentSpotDesignReadSpecComparator
compare(ModuleInterface, ModuleInterface) - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin.ModuleComparator
 
compare(PluginInterface, PluginInterface) - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin.PluginComparator
 
compare(Object, Object) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators.ContigPositionComparator
compare(Object, Object) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators.IntegerIdComparator
compare(Object, Object) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators.TagComparator
CompareDatabasesWithROC - Class in net.sourceforge.seqware.queryengine.examples
CompareDatabasesWithROC class.
CompareDatabasesWithROC() - Constructor for class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROC
 
CompareDatabasesWithROCHBase - Class in net.sourceforge.seqware.queryengine.examples
CompareDatabasesWithROCHBase class.
CompareDatabasesWithROCHBase() - Constructor for class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROCHBase
 
CompareDatabasesWithROCOld - Class in net.sourceforge.seqware.queryengine.examples
CompareDatabasesWithROCOld class.
CompareDatabasesWithROCOld() - Constructor for class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROCOld
 
compareTo(SequencerRunReport.Row) - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
compareTo(Expense) - Method in class net.sourceforge.seqware.common.model.Expense
compareTo(Experiment) - Method in class net.sourceforge.seqware.common.model.Experiment
compareTo(ExperimentAttribute) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
compareTo(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
compareTo.
compareTo(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
compareTo.
compareTo(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
compareTo(File) - Method in class net.sourceforge.seqware.common.model.File
compareTo(FileType) - Method in class net.sourceforge.seqware.common.model.FileType
compareTo(Invoice) - Method in class net.sourceforge.seqware.common.model.Invoice
compareTo(IUS) - Method in class net.sourceforge.seqware.common.model.IUS
compareTo(IUSAttribute) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
compareTo(Lane) - Method in class net.sourceforge.seqware.common.model.Lane
compareTo(LaneAttribute) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
compareTo(LibrarySelection) - Method in class net.sourceforge.seqware.common.model.LibrarySelection
compareTo(LibrarySource) - Method in class net.sourceforge.seqware.common.model.LibrarySource
compareTo(LibraryStrategy) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
compareTo(Organism) - Method in class net.sourceforge.seqware.common.model.Organism
compareTo(Platform) - Method in class net.sourceforge.seqware.common.model.Platform
compareTo(Processing) - Method in class net.sourceforge.seqware.common.model.Processing
compareTo(ProcessingAttribute) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
compareTo(Registration) - Method in class net.sourceforge.seqware.common.model.Registration
compareTo(Sample) - Method in class net.sourceforge.seqware.common.model.Sample
compareTo(SampleAttribute) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
compareTo(SequencerRun) - Method in class net.sourceforge.seqware.common.model.SequencerRun
compareTo(SequencerRunAttribute) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
compareTo(ShareStudy) - Method in class net.sourceforge.seqware.common.model.ShareStudy
compareTo(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
compareTo(Study) - Method in class net.sourceforge.seqware.common.model.Study
compareTo.
compareTo(StudyAttribute) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
compareTo(StudyType) - Method in class net.sourceforge.seqware.common.model.StudyType
compareTo.
compareTo(Workflow) - Method in class net.sourceforge.seqware.common.model.Workflow
compareTo(WorkflowAttribute) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
compareTo(WorkflowParam) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
compareTo(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
compareTo(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
compareTo.
compareTo(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
compareTo(WorkflowRunAttribute) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
compareTo(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
compareTo(StudySampleReportFileLineItem) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
compareTo(StudySampleReportLineItem) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
CompareTwoVariantAndCoverageDatabases - Class in net.sourceforge.seqware.queryengine.tools.reporters
CompareTwoVariantAndCoverageDatabases class.
CompareTwoVariantAndCoverageDatabases() - Constructor for class net.sourceforge.seqware.queryengine.tools.reporters.CompareTwoVariantAndCoverageDatabases
 
CompareTwoVariantDatabases - Class in net.sourceforge.seqware.queryengine.tools.reporters
CompareTwoVariantDatabases class.
CompareTwoVariantDatabases() - Constructor for class net.sourceforge.seqware.queryengine.tools.reporters.CompareTwoVariantDatabases
 
compareWorkflowRunFiles(int, Collection<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
Tests if the files from the workflow run (workflowRunAcc) are the same as those found in the database (filesToRun).
comparison() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
comparison.
compileQuery(String) - Static method in class com.github.seqware.queryengine.kernel.RPNStack
Compiles the given query string that adheres to the syntax of SeqWareQueryLanguage.g and returns a RPNStack object representing the query.
COMPLETED - Static variable in class net.sourceforge.seqware.common.metadata.Metadata
Constant COMPLETED="completed"
compressed - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
COMPRESSED_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
Constant COMPRESSED_PARAM='c'
Compression - Class in com.github.seqware.queryengine.kernel
Static methods for compressing/decompressing user data.
Compression() - Constructor for class com.github.seqware.queryengine.kernel.Compression
 
config - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
config - Variable in class net.sourceforge.seqware.pipeline.decider.Decider
 
config - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
config - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
config - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
configs - Variable in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
ConfigTools - Class in net.sourceforge.seqware.common.util.configtools
ConfigTools class.
ConfigTools() - Constructor for class net.sourceforge.seqware.common.util.configtools.ConfigTools
 
configureHBaseConfig(Configuration) - Static method in class com.github.seqware.queryengine.impl.HBaseStorage
Configure a HBaseConfiguration with a given set of properties
consensusAveSeqQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
consensusBase - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
consensusCallQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
consensusMaxSeqQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
Consequence - Class in net.sourceforge.seqware.queryengine.backend.model
Consequence class.
Consequence() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
CONSEQUENCE - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model
Constant CONSEQUENCE=60
ConsequenceResource - Class in net.sourceforge.seqware.queryengine.webservice.view
ConsequenceResource class.
ConsequenceResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.ConsequenceResource
 
ConsequenceTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders
ConsequenceTB class.
ConsequenceTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.ConsequenceTB
 
ConsequenceVariantIdKeyCreator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators
ConsequenceVariantIdKeyCreator class.
ConsequenceVariantIdKeyCreator(TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.ConsequenceVariantIdKeyCreator
Constructor for ConsequenceVariantIdKeyCreator.
ConsoleAdapter - Class in net.sourceforge.seqware.common.util.runtools
 
ConsoleAdapter() - Constructor for class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter
 
consolidateRow(List<FeatureList>) - Static method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
Given a collection of FeatureLists all with the same row key (and differing timestamps), create a consistent view of the features in the feature set corresponding effectively to the last timestamp
CONST_AT_SIGN - Static variable in class net.sourceforge.solexatools.validation.LoginValidator
Constant CONST_AT_SIGN="@"
constant() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
constant.
Constant - Class in net.sourceforge.solexatools.util
Constant class.
Constant() - Constructor for class net.sourceforge.solexatools.util.Constant
 
Constants - Class in com.github.seqware.queryengine
Defaults for our Constants are defined here and can be overridden by entries in the ~/.seqware/settings file.
Constants() - Constructor for class com.github.seqware.queryengine.Constants
 
Constants.Term - Enum in com.github.seqware.queryengine
 
constraint() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
constraint.
constructCommand() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
contact - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS
 
contacts - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
containsKey(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
containsKey.
containsKey(String) - Method in interface com.github.seqware.queryengine.model.TagSet
containsKey.
ContextImpl - Class in net.sourceforge.seqware.common
ContextImpl class.
contig - Variable in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
 
contig - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
ContigPosition - Class in net.sourceforge.seqware.queryengine.backend.model
ContigPosition class.
ContigPosition() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.ContigPosition
 
CONTIGPOSITION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model
Constant CONTIGPOSITION=50
ContigPositionComparator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators
ContigPositionComparator class.
ContigPositionComparator() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators.ContigPositionComparator
 
ContigPositionKeyCreator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators
ContigPositionKeyCreator class.
ContigPositionKeyCreator(TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.ContigPositionKeyCreator
Constructor for ContigPositionKeyCreator.
ContigPositionTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders
ContigPositionTB class.
ContigPositionTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.ContigPositionTB
 
ControllerUtil - Class in net.sourceforge.solexatools.util
ControllerUtil class.
ControllerUtil() - Constructor for class net.sourceforge.solexatools.util.ControllerUtil
 
copy(boolean) - Method in interface com.github.seqware.queryengine.model.Atom
Copy constructor, used to generate a shallow copy of a Atom ith potentially a new timestamp and UUID
copy(boolean) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Copy constructor, used to generate a shallow copy of a Atom ith potentially a new timestamp and UUID
copyBundle(String, String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
copyBundle.
copyBundleToS3(File, String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
copyBundleToS3.
copyFromLocal(FileSystem, String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine
 
copyInputStream(InputStream, OutputStream) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
copyInputStream.
copyInputStream(InputStream, OutputStream) - Static method in class net.sourceforge.solexatools.util.ZipFileUtil
copyInputStream.
copyProperty(Object, String, Object) - Method in class net.sourceforge.seqware.common.util.NullBeanUtils
copyToFile(BufferedInputStream, String, int, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
copyToFile(BufferedInputStream, String, boolean, int, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Copy reader into output.
copyToFile(BufferedInputStream, String, boolean, int, String, Cipher, Cipher) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Copy reader into output using Cipher.
count - Variable in class net.sourceforge.seqware.queryengine.backend.model.Coverage
 
countOfRows(Study) - Method in interface net.sourceforge.seqware.common.business.FileReportService
countOfRows.
countOfRows(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.FileReportService
countOfRows.
countOfRows(Study) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
countOfRows.
countOfRows(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
countOfRows.
countOfRows(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
countOfRows.
countOfRows(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
countOfRows.
countOfRows(Study) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
countOfRows.
countOfRows(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
countOfRows.
countOfRows(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
countOfRows.
countOfRows(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
countOfRows.
countOfRows(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
countOfRows.
countOfRows(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
countOfRows.
countOfStatus(Study, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
countOfStatus.
countOfStatus(SequencerRun, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
countOfStatus.
countOfStatus(Study, Workflow, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
countOfStatus.
countOfStatus(SequencerRun, Workflow, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
countOfStatus.
countOfStatus(Study, String) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
countOfStatus.
countOfStatus(Study, Workflow, String) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
countOfStatus.
countOfStatus(SequencerRun, String) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
countOfStatus.
countOfStatus(SequencerRun, Workflow, String) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
countOfStatus.
countOfStatus(Study, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
countOfStatus.
countOfStatus(Study, Workflow, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
countOfStatus.
countOfStatus(SequencerRun, Workflow, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
countOfStatus.
countOfStatus(SequencerRun, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
countOfStatus.
countOfStatus(Study, String) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
countOfStatus.
countOfStatus(SequencerRun, String) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
countOfStatus.
countOfStatus(Study, Workflow, String) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
countOfStatus.
countOfStatus(SequencerRun, Workflow, String) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
countOfStatus.
Coverage - Class in net.sourceforge.seqware.queryengine.backend.model
Coverage class.
Coverage() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.Coverage
 
coverage - Variable in class net.sourceforge.seqware.queryengine.backend.model.Coverage
 
COVERAGE - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model
Constant COVERAGE=40
CoverageIteratorProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators
CoverageIteratorProcessor class.
CoverageIteratorProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.CoverageIteratorProcessor
 
CoverageProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators.processors
CoverageProcessor class.
CoverageProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
 
CoverageResource - Class in net.sourceforge.seqware.queryengine.webservice.view
CoverageResource class.
CoverageResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.CoverageResource
 
CoveragesResource - Class in net.sourceforge.seqware.queryengine.webservice.view
CoveragesResource class.
CoveragesResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.CoveragesResource
 
CoverageStatsProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators.processors
CoverageStatsProcessor class.
CoverageStatsProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageStatsProcessor
 
CoverageTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders
CoverageTB class.
CoverageTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.CoverageTB
 
create(SampleSearch) - Method in class net.sourceforge.seqware.common.business.impl.SampleSearchServiceImpl
create.
create(SampleSearch) - Method in interface net.sourceforge.seqware.common.business.SampleSearchService
create.
create(SampleSearch) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleSearchDAOHibernate
create.
create(SampleSearch) - Method in interface net.sourceforge.seqware.common.dao.SampleSearchDAO
create.
create() - Static method in class net.sourceforge.seqware.common.util.testtools.JndiDatasourceCreator
create.
createANALYSIS(AnalysisType) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of JAXBElement<AnalysisType>}
createANALYSISSET() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisSet
createAnalysisType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType
createAnalysisTypeANALYSISATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISATTRIBUTES
createAnalysisTypeANALYSISATTRIBUTESANALYSISATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
createAnalysisTypeANALYSISFILES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISFILES
createAnalysisTypeANALYSISFILESFILE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISFILES.FILE
createAnalysisTypeANALYSISLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISLINKS
createAnalysisTypeANALYSISLINKSANALYSISLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISLINKS.ANALYSISLINK
createAnalysisTypeANALYSISLINKSANALYSISLINKENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
createAnalysisTypeANALYSISLINKSANALYSISLINKURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
createAnalysisTypeANALYSISLINKSANALYSISLINKXREFLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
createAnalysisTypeANALYSISTYPE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.ANALYSISTYPE
createAnalysisTypePARENT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.PARENT
createAnalysisTypePARENTEXPERIMENTREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.PARENT.EXPERIMENTREF
createAnalysisTypePARENTRUNREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.PARENT.RUNREF
createAnalysisTypePARENTSAMPLEPOOLREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.PARENT.SAMPLEPOOLREF
createAnalysisTypePARENTSAMPLEPOOLREFMEMBER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
createAnalysisTypePARENTSAMPLEREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.PARENT.SAMPLEREF
createAnalysisTypePARENTSTUDYREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of AnalysisType.PARENT.STUDYREF
createBashJob(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
createDatabase() - Static method in class net.sourceforge.seqware.common.util.testtools.DatabaseCreator
createDatabase.
createDatabase() - Static method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator
createDatabase.
createDirectoryWithUniqueName(File, String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
createDirectoryWithUniqueName.
createEXPERIMENT(ExperimentType) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of JAXBElement<ExperimentType>}
createEXPERIMENTSET() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentSet
createExperimentType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType
createExperimentTypeDESIGN() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.DESIGN
createExperimentTypeDESIGNLIBRARYDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.DESIGN.LIBRARYDESCRIPTOR
createExperimentTypeDESIGNLIBRARYDESCRIPTORLIBRARYLAYOUT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
createExperimentTypeDESIGNLIBRARYDESCRIPTORLIBRARYLAYOUTPAIRED() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
createExperimentTypeDESIGNSAMPLEDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.DESIGN.SAMPLEDESCRIPTOR
createExperimentTypeDESIGNSPOTDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.DESIGN.SPOTDESCRIPTOR
createExperimentTypeDESIGNSPOTDESCRIPTORSPOTDECODESPEC() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
createExperimentTypeDESIGNSPOTDESCRIPTORSPOTDECODESPECREADSPEC() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
createExperimentTypeEXPERIMENTATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.EXPERIMENTATTRIBUTES
createExperimentTypeEXPERIMENTATTRIBUTESEXPERIMENTATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
createExperimentTypeEXPERIMENTLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.EXPERIMENTLINKS
createExperimentTypeEXPERIMENTLINKSEXPERIMENTLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
createExperimentTypeEXPERIMENTLINKSEXPERIMENTLINKENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
createExperimentTypeEXPERIMENTLINKSEXPERIMENTLINKURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
createExperimentTypePLATFORM() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PLATFORM
createExperimentTypePLATFORMABISOLID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PLATFORM.ABISOLID
createExperimentTypePLATFORMABISOLIDCOLORMATRIX() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PLATFORM.ABISOLID.COLORMATRIX
createExperimentTypePLATFORMABISOLIDCOLORMATRIXCOLOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
createExperimentTypePLATFORMHELICOS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PLATFORM.HELICOS
createExperimentTypePLATFORMILLUMINA() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PLATFORM.ILLUMINA
createExperimentTypePLATFORMLS454() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PLATFORM.LS454
createExperimentTypePROCESSING() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PROCESSING
createExperimentTypePROCESSINGBASECALLS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PROCESSING.BASECALLS
createExperimentTypePROCESSINGQUALITYSCORES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.PROCESSING.QUALITYSCORES
createExperimentTypeSTUDYREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of ExperimentType.STUDYREF
createFile(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
create a sqwfile
createFileWithUniqueName(File, String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
createFileWithUniqueName.
createInboundRoot() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication
Creates a root Restlet that will receive all incoming calls.
createInboundRoot() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion
Creates a root Restlet that will receive all incoming calls.
createINI(HashMap<String, String>) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowManager
createINI.
createJavaJob(String, String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
createJavaSeqwareModuleJob(String, String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
createKey(Atom) - Static method in class com.github.seqware.queryengine.impl.NonPersistentStorage
createKey.
createKey(SGID) - Static method in class com.github.seqware.queryengine.impl.NonPersistentStorage
createKey.
createKey(SGID, boolean) - Static method in class com.github.seqware.queryengine.impl.NonPersistentStorage
createKey.
createPerlJob(String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
createRUN(RunType) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of JAXBElement<RunType>}
createRUNSET() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunSet
createRunType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType
createRunTypeDATABLOCK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.DATABLOCK
createRunTypeDATABLOCKFILES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.DATABLOCK.FILES
createRunTypeDATABLOCKFILESFILE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.DATABLOCK.FILES.FILE
createRunTypeEXPERIMENTREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.EXPERIMENTREF
createRunTypeRUNATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.RUNATTRIBUTES
createRunTypeRUNATTRIBUTESRUNATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.RUNATTRIBUTES.RUNATTRIBUTE
createRunTypeRUNLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.RUNLINKS
createRunTypeRUNLINKSRUNLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.RUNLINKS.RUNLINK
createRunTypeRUNLINKSRUNLINKENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.RUNLINKS.RUNLINK.ENTREZLINK
createRunTypeRUNLINKSRUNLINKURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of RunType.RUNLINKS.RUNLINK.URLLINK
createSAMPLE(SampleType) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of JAXBElement<SampleType>}
createSAMPLESET() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleSet
createSampleType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType
createSampleTypeMEMBERS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType.MEMBERS
createSampleTypeMEMBERSMEMBER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType.MEMBERS.MEMBER
createSampleTypeSAMPLEATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType.SAMPLEATTRIBUTES
createSampleTypeSAMPLEATTRIBUTESSAMPLEATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
createSampleTypeSAMPLELINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType.SAMPLELINKS
createSampleTypeSAMPLELINKSSAMPLELINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType.SAMPLELINKS.SAMPLELINK
createSampleTypeSAMPLELINKSSAMPLELINKENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
createSampleTypeSAMPLELINKSSAMPLELINKURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
createSampleTypeSAMPLENAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SampleType.SAMPLENAME
createSecondaryKey(SecondaryDatabase, DatabaseEntry, DatabaseEntry, DatabaseEntry) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.ConsequenceVariantIdKeyCreator
createSecondaryKey(SecondaryDatabase, DatabaseEntry, DatabaseEntry, DatabaseEntry) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.ContigPositionKeyCreator
createSecondaryKeys(SecondaryDatabase, DatabaseEntry, DatabaseEntry, Set) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.TagKeyCreator
createSecondaryKeys(SecondaryDatabase, DatabaseEntry, DatabaseEntry, Set) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.TagKeyOnlyCreator
createSTUDY(StudyType) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of JAXBElement<StudyType>}
createSTUDYSET() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudySet
createStudyType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudyType
createStudyTypeDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudyType.DESCRIPTOR
createStudyTypeDESCRIPTORSTUDYABSTRACT(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of JAXBElement<String>}
createStudyTypeDESCRIPTORSTUDYTYPE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudyType.DESCRIPTOR.STUDYTYPE
createStudyTypeSTUDYATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudyType.STUDYATTRIBUTES
createStudyTypeSTUDYATTRIBUTESSTUDYATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
createStudyTypeSTUDYLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudyType.STUDYLINKS
createStudyTypeSTUDYLINKSSTUDYLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudyType.STUDYLINKS.STUDYLINK
createStudyTypeSTUDYLINKSSTUDYLINKENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
createStudyTypeSTUDYLINKSSTUDYLINKURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of StudyType.STUDYLINKS.STUDYLINK.URLLINK
createSUBMISSION(SubmissionType) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of JAXBElement<SubmissionType>}
createSUBMISSIONSET() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionSet
createSubmissionType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType
createSubmissionTypeACTIONS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.ACTIONS
createSubmissionTypeACTIONSACTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.ACTIONS.ACTION
createSubmissionTypeACTIONSACTIONADD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.ACTIONS.ACTION.ADD
createSubmissionTypeACTIONSACTIONHOLD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.ACTIONS.ACTION.HOLD
createSubmissionTypeACTIONSACTIONMODIFY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.ACTIONS.ACTION.MODIFY
createSubmissionTypeACTIONSACTIONRELEASE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.ACTIONS.ACTION.RELEASE
createSubmissionTypeACTIONSACTIONSUPPRESS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.ACTIONS.ACTION.SUPPRESS
createSubmissionTypeACTIONSACTIONVALIDATE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.ACTIONS.ACTION.VALIDATE
createSubmissionTypeCONTACTS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.CONTACTS
createSubmissionTypeCONTACTSCONTACT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.CONTACTS.CONTACT
createSubmissionTypeFILES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.FILES
createSubmissionTypeFILESFILE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create an instance of SubmissionType.FILES.FILE
createSubmittableJob(Configuration, String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.MapReduceTest
Sets up the actual job.
createSubmittableJob(Configuration, String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.MapReduceTest2
Sets up the actual job.
createSymlink(String, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
createSymlink(String, boolean, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Creates symlink of input to output.
createTargetDirectory(String, String) - Static method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Creates abstract pathname.
createTargetPath(String, String, String) - Static method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Creates abstract pathname.
createTempDirectory(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
createTempDirectory.
CreateUpdateManager - Interface in com.github.seqware.queryengine.factory
A very simple Manager that is somewhat like a very stripped down EntityManager from JPA allowing us to create Models and persist them, in other words this handles Create and Update operations out of the basic CRUD operations.
CreateUpdateManager.State - Enum in com.github.seqware.queryengine.factory
This manager defines Atoms to be in the following states
createWorkflow() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
 
CSV_TYPE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant CSV_TYPE="csvtype"
CSV_TYPE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
Constant CSV_TYPE="csvtype"
currGenomeTagIndexTable - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
currStep - Variable in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
 
currStep - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
CursorIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators
CursorIterator class.
CursorIterator(Cursor, TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator
Constructor for CursorIterator.
CustomIntegerEditor - Class in net.sourceforge.solexatools.validation
CustomIntegerEditor class.
CustomIntegerEditor() - Constructor for class net.sourceforge.solexatools.validation.CustomIntegerEditor
Constructor for CustomIntegerEditor.
CycleChecker - Class in net.sourceforge.seqware.pipeline.plugins
CycleChecker class.
CycleChecker() - Constructor for class net.sourceforge.seqware.pipeline.plugins.CycleChecker
Constructor for CycleChecker.
CycleCheckResource - Class in net.sourceforge.seqware.webservice.resources.queries
CycleCheckResource class.
CycleCheckResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.CycleCheckResource
Constructor for CycleCheckResource.
cyclecoord - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
 
cyclecount - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
 
cyclecount - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
 
cyclesequence - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
 

D

data - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
DatabaseCreator - Class in net.sourceforge.seqware.common.util.testtools
DatabaseCreator class.
DatabaseCreator() - Constructor for class net.sourceforge.seqware.common.util.testtools.DatabaseCreator
 
DatabaseIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
DatabaseIDResource class.
DatabaseIDResource(String) - Constructor for class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
Constructor for DatabaseIDResource.
DatabaseResource - Class in net.sourceforge.seqware.webservice.resources.tables
DatabaseResource class.
DatabaseResource(String) - Constructor for class net.sourceforge.seqware.webservice.resources.tables.DatabaseResource
Constructor for DatabaseResource.
datablock - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
dataDecryptionKey - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
dataEncryptionKey - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
dataEncryptionKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
dataSource() - Method in class net.sourceforge.seqware.pipeline.runner.DefaultConfig
dataSource.
DATE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
DATE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
Daxgenerator - Class in net.sourceforge.seqware.pipeline.daxgenerator
Daxgenerator class.
Daxgenerator() - Constructor for class net.sourceforge.seqware.pipeline.daxgenerator.Daxgenerator
 
DaxgeneratorV2 - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus
 
DaxgeneratorV2() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.DaxgeneratorV2
 
db - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
 
db - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
 
db - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
 
db - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK
 
db - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
 
db - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
 
DB_CONN_STRING - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
 
DB_NAME - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
 
DB_PASS - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
 
DB_SERVER - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
 
DB_USER - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
 
DBAccess - Class in net.sourceforge.seqware.common.factory
DBAccess class.
DBCOULDNOTDISCONNECT - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant DBCOULDNOTDISCONNECT=81
DBCOULDNOTINITIALIZE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant DBCOULDNOTINITIALIZE=80
DEBUG - Static variable in class com.github.seqware.queryengine.impl.HBaseStorage
Constant DEBUG=true
debug(Object) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.debug(Object).
debug(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.debug(Object,Throwable).
debug - Variable in class net.sourceforge.seqware.queryengine.backend.util.SeqWareBase
 
Debug - Class in net.sourceforge.solexatools
Debug class.
Debug() - Constructor for class net.sourceforge.solexatools.Debug
 
Decider - Class in net.sourceforge.seqware.pipeline.decider
Abstract Decider class.
Decider() - Constructor for class net.sourceforge.seqware.pipeline.decider.Decider
Notes: Things I would like taken care of for me: * all params in a hash (from both DB and ini file provided) * a list of hashmap that represent a filtered list of files by sample, study, experiment, workflow, etc * a list of files that represent the output from this workflow * a hash that joins the output of this workflow to their parents * the master list of results should be configurable, either to have all the processing events removed where this workflow has already been run or to include these
DeciderInterface - Interface in net.sourceforge.seqware.pipeline.decider
DeciderInterface interface.
DefaultConfig - Class in net.sourceforge.seqware.pipeline.runner
Default Configuation class.
DefaultConfig() - Constructor for class net.sourceforge.seqware.pipeline.runner.DefaultConfig
 
delete(Experiment, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
delete.
delete(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
delete.
delete(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService
delete.
delete(File, String) - Method in interface net.sourceforge.seqware.common.business.FileService
delete.
delete(Experiment, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
delete.
delete(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl
delete.
delete(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl
delete.
delete(File, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
delete.
delete(Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
delete.
delete(IUS, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
delete.
delete(Lane, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
delete.
delete(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
delete.
delete(ProcessingIus) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
delete.
delete(ProcessingLanes) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
delete.
delete(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
delete.
delete(ProcessingSamples) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
delete.
delete(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
delete.
delete(Processing, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
delete.
delete(ProcessingStudies) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
delete.
delete(Sample, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
delete.
delete(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
delete.
delete(ShareExperiment) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
delete.
delete(ShareFile) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
delete.
delete(ShareLane) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
delete.
delete(ShareProcessing) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
delete.
delete(ShareSample) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
delete.
delete(ShareStudy) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
delete.
delete(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
delete.
delete(Study, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
delete.
delete(WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
delete.
delete(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
delete.
delete(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
delete.
delete(WorkflowRun, String) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
delete.
delete(Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
delete.
delete(Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
delete.
delete(IUS, String) - Method in interface net.sourceforge.seqware.common.business.IUSService
delete.
delete(Lane, String) - Method in interface net.sourceforge.seqware.common.business.LaneService
delete.
delete(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService
delete.
delete(ProcessingIus) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService
delete.
delete(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService
delete.
delete(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService
delete.
delete(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService
delete.
delete(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService
delete.
delete(Processing, String) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
delete.
delete(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService
delete.
delete(Sample, String) - Method in interface net.sourceforge.seqware.common.business.SampleService
delete.
delete(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
delete.
delete(ShareExperiment) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
delete.
delete(ShareFile) - Method in interface net.sourceforge.seqware.common.business.ShareFileService
delete.
delete(ShareLane) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
delete.
delete(ShareProcessing) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
delete.
delete(ShareSample) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
delete.
delete(ShareStudy) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
delete.
delete(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
delete.
delete(Study, String) - Method in interface net.sourceforge.seqware.common.business.StudyService
delete.
delete(WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
delete.
delete(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
delete.
delete(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
delete.
delete(WorkflowRun, String) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
delete.
delete(Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
delete.
delete(ExperimentAttribute) - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO
delete.
delete(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
delete.
delete(ExperimentLink) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO
delete.
delete(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO
delete.
delete(FileAttribute) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO
delete.
delete(File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
delete.
delete(ExperimentAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate
delete.
delete(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
delete.
delete(ExperimentLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate
delete.
delete(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate
delete.
delete(FileAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
delete.
delete(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
delete.
delete(Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
delete.
delete(IUSAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate
delete.
delete(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
delete.
delete(IUSLink) - Method in interface net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAO
delete.
delete(IUSLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate
delete.
delete(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAO
delete.
delete(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate
delete.
delete(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
delete.
delete(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
delete.
delete(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAO
delete.
delete(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate
delete.
delete(ProcessingAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate
delete.
delete(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
delete.
delete(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate
delete.
delete(ProcessingIus) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate
delete.
delete(ProcessingLanes) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate
delete.
delete(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate
delete.
delete(ProcessingSamples) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate
delete.
delete(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate
delete.
delete(ProcessingStudies) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate
delete.
delete(SampleAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate
delete.
delete(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
delete.
delete(SampleLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate
delete.
delete(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
delete.
delete(ShareExperiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
delete.
delete(ShareFile) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
delete.
delete(ShareLane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
delete.
delete(ShareProcessing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
delete.
delete(ShareSample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
delete.
delete(ShareStudy) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate
delete.
delete(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
delete.
delete(StudyAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate
delete.
delete(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
delete.
delete(StudyLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate
delete.
delete(WorkflowAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
delete.
delete(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
delete.
delete(WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
delete.
delete(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
delete.
delete(WorkflowRunAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
delete.
delete(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
delete.
delete(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
delete.
delete(Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
delete.
delete(IUSAttribute) - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO
delete.
delete(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
delete.
delete(Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
delete.
delete(SortedSet<Lane>) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
delete.
delete(ProcessingAttribute) - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO
delete.
delete(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
delete.
delete(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO
delete.
delete(ProcessingIus) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO
delete.
delete(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO
delete.
delete(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO
delete.
delete(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO
delete.
delete(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO
delete.
delete(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO
delete.
delete(SampleAttribute) - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO
delete.
delete(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
delete.
delete(SampleLink) - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO
delete.
delete(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
delete.
delete(ShareExperiment) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO
delete.
delete(ShareFile) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO
delete.
delete(ShareLane) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO
delete.
delete(ShareProcessing) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO
delete.
delete(ShareSample) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO
delete.
delete(ShareStudy) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO
delete.
delete(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
delete.
delete(StudyAttribute) - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO
delete.
delete(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
delete.
delete(StudyLink) - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO
delete.
delete(WorkflowAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
delete.
delete(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
delete.
delete(WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO
delete.
delete(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
delete.
delete(WorkflowRunAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
delete.
delete(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
delete.
delete(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
delete.
delete() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunIDsFilter
delete() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
delete() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
deleteAll(List<File>, String) - Method in interface net.sourceforge.seqware.common.business.FileService
deleteAll.
deleteAll(List<File>, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
deleteAll.
deleteAll(List<File>) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
deleteAll.
deleteAll(List<File>) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
deleteAll.
deleteAllWithFolderStore(List<File>) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
deleteAllWithFolderStore.
deleteAllWithFolderStore(List<File>) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
deleteAllWithFolderStore.
deleteAttribute() - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributeResource
deleteAttribute.
deleteAttribute() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource
deleteAttribute.
deleteDirectoryRecursive(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
deleteDirectoryRecursive.
DeleteLoadedIndexPageController - Class in net.sourceforge.solexatools.webapp.controller
DeleteLoadedIndexPageController class.
DeleteLoadedIndexPageController() - Constructor for class net.sourceforge.solexatools.webapp.controller.DeleteLoadedIndexPageController
Constructor for DeleteLoadedIndexPageController.
DeleteTempFile(Registration) - Method in class net.sourceforge.solexatools.webapp.controller.LoginController
DeleteTempFile.
DELETION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant DELETION=3
denovoassembly - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
 
describeInterfaceAndImplementation(Object, String) - Static method in class net.sourceforge.solexatools.Debug
describeInterfaceAndImplementation.
description - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
description - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
description - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
 
DESCRIPTION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
DESCRIPTION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
DESCRIPTION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
descriptor - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
 
deserialize(byte[], Class<T>) - Method in interface com.github.seqware.queryengine.backInterfaces.SerializationInterface
Given an array of bytes, get back an atom
deserialize(byte[], Class<T>) - Method in class com.github.seqware.queryengine.impl.ApacheSerialization
Given an array of bytes, get back an atom
deserialize(byte[], Class<T>) - Method in class com.github.seqware.queryengine.impl.KryoSerialization
Given an array of bytes, get back an atom
deserialize(byte[], Class<T>) - Method in class com.github.seqware.queryengine.impl.ProtobufSerialization
Given an array of bytes, get back an atom
deserializeTargetToAtom(SGID) - Method in class com.github.seqware.queryengine.backInterfaces.StorageInterface
Generically get back a Atom from the store using a sgid
deserializeTargetToAtom(Class<T>, SGID) - Method in class com.github.seqware.queryengine.backInterfaces.StorageInterface
Generically get back a specific class of Atom from the store using a sgid
deserializeTargetToAtom(SGID) - Method in class com.github.seqware.queryengine.impl.HBaseStorage
Generically get back a Atom from the store using a sgid
deserializeTargetToAtom(Class<T>, SGID) - Method in class com.github.seqware.queryengine.impl.HBaseStorage
Generically get back a specific class of Atom from the store using a sgid
deserializeTargetToAtom(SGID) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
Generically get back a Atom from the store using a sgid
deserializeTargetToAtom(Class<T>, SGID) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
Generically get back a specific class of Atom from the store using a sgid
deserializeTargetToAtom(SGID) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
Generically get back a Atom from the store using a sgid
deserializeTargetToAtom(Class<T>, SGID) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
Generically get back a specific class of Atom from the store using a sgid
deserializeTargetToAtoms(Class<T>, SGID...) - Method in class com.github.seqware.queryengine.backInterfaces.StorageInterface
Generically get back a specific class of Atom from the store using a sgid
deserializeTargetToAtoms(Class<T>, SGID...) - Method in class com.github.seqware.queryengine.impl.HBaseStorage
Generically get back a specific class of Atom from the store using a sgid
deserializeTargetToAtoms(Class<T>, SGID...) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
Generically get back a specific class of Atom from the store using a sgid
deserializeTargetToAtoms(Class<T>, SGID...) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
Generically get back a specific class of Atom from the store using a sgid
deserializeTargetToLatestAtom(SGID) - Method in class com.github.seqware.queryengine.backInterfaces.StorageInterface
Generically get back the latest Atom in a chain from the store using a sgid while ignoring the timestamp
deserializeTargetToLatestAtom(SGID, Class<T>) - Method in class com.github.seqware.queryengine.backInterfaces.StorageInterface
Generically get back a specific class of Atom from the store using a sgid while ignoring the timestamp to get the latest one
deserializeTargetToLatestAtom(SGID) - Method in class com.github.seqware.queryengine.impl.HBaseStorage
Generically get back the latest Atom in a chain from the store using a sgid while ignoring the timestamp
deserializeTargetToLatestAtom(SGID, Class<T>) - Method in class com.github.seqware.queryengine.impl.HBaseStorage
Generically get back a specific class of Atom from the store using a sgid while ignoring the timestamp to get the latest one
deserializeTargetToLatestAtom(SGID) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
Generically get back the latest Atom in a chain from the store using a sgid while ignoring the timestamp
deserializeTargetToLatestAtom(SGID, Class<T>) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
Generically get back a specific class of Atom from the store using a sgid while ignoring the timestamp to get the latest one
deserializeTargetToLatestAtom(SGID) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
Generically get back the latest Atom in a chain from the store using a sgid while ignoring the timestamp
deserializeTargetToLatestAtom(SGID, Class<T>) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
Generically get back a specific class of Atom from the store using a sgid while ignoring the timestamp to get the latest one
design - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
designdescription - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
 
destSet - Variable in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner.PluginRunnerMapper
the feature set that we will be writing to, may be null
determineFilePermissions(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
This tool uses the 'ls -al' command to find the current file permissions.
determineRelativeBundlePath(OptionSet) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility
Determine the bundle path from the provided options
determineStatus(int) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
Determines whether a workflow run completed, failed, or other (submitted, pending, etc.)
dfa14 - Variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
 
dibase - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
 
directBIMap - Variable in class com.github.seqware.queryengine.backInterfaces.StorageInterface
These tables are always created with the same names
DIRECTORYNOTREADABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant DIRECTORYNOTREADABLE=3
DIRECTORYNOTWRITABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant DIRECTORYNOTWRITABLE=11
dirPathExistsAndReadable(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
dirPathExistsAndReadable.
dirPathExistsAndWritable(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
dirPathExistsAndWritable.
dissociateTag(Tag) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Remove a new tag from a subject
dissociateTag(Tag) - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable
Remove a new tag from a subject
dissociateTag(Tag) - Method in class com.github.seqware.queryengine.model.Tag
Remove a new tag from a subject
do_run() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider
Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
do_run() - Method in class net.sourceforge.seqware.pipeline.module.Module
do_run.
do_run() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
Performs the main tasks for the module.
do_run() - Method in class net.sourceforge.seqware.pipeline.module.TestModule
do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory
 
do_run() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
 
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator
Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection
Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager
Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker
Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker
 
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner
Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.OozieXML2Dot
 
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot
 
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter
Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter
Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter
Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
Performs the main tasks for the plugin.
do_summary() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Just returns a summary of what would be run.
do_summary() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
do_test() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider
Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
do_test() - Method in class net.sourceforge.seqware.pipeline.module.Module
do_test.
do_test() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.module.TestModule
do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory
Things to check: * FIXME
do_test() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
 
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator
Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection
Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager
Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker
Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker
 
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner
Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.OozieXML2Dot
 
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot
 
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter
Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter
Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter
Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
Perform any active system testing here.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.module.Module
do_verify_input.
do_verify_input() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
Input data validation code goes here.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.module.TestModule
do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory
 
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.module.Module
do_verify_output.
do_verify_output() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
Perform post-task tests here.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.module.TestModule
do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory
 
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.module.Module
do_verify_parameters.
do_verify_parameters() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
Parameter validation code goes here.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.module.TestModule
do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory
 
doCreateTableJson(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
doCreateTableJson.
doFinalCheck(String, String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
allow to user to do the final check and decide to run or cancel the decider e.g.
doInit() - Method in class net.sourceforge.seqware.webservice.resources.BasicResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.filters.StudyIDFilter
doInit() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunIDsFilter
doInit() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter
doInit() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileLinkReportResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileReverseHierarchyDisplayResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusFilesServerResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusSearchServerResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrariesResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibraryResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrarySelectionResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrarySourceResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibraryStrategyResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.OrganismResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.PlatformResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.RootSampleResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyTypeResource
doOldRun() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
This is the original run method from the old Workflow launcher.
doRetrieveListElements(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
doRetrieveListElements.
doRun() - Method in class net.sourceforge.seqware.pipeline.runner.LogAspect
doRun.
doRun() - Method in class net.sourceforge.seqware.pipeline.runner.RedirectAspect
doRun.
doSetupReport(HttpServletRequest) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportSetupController
doSetupReport.
DownloaderController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
DownloaderController() - Constructor for class net.sourceforge.solexatools.webapp.controller.DownloaderController
Constructor for DownloaderController.
DownloadFileListController - Class in net.sourceforge.solexatools.webapp.controller
DownloadFileListController class.
DownloadFileListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
Constructor for DownloadFileListController.
dropDatabase() - Static method in class net.sourceforge.seqware.common.util.testtools.DatabaseCreator
dropDatabase.
dropDatabase() - Static method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator
dropDatabase.
Dtos - Class in net.sourceforge.seqware.webservice.dto
Methods to convert between domain objects and dtos.
Dtos() - Constructor for class net.sourceforge.seqware.webservice.dto.Dtos
 
dumpVCFFromFeatureSetID(FeatureSet, String) - Static method in class com.github.seqware.queryengine.system.exporters.VCFDumper
dumpVCFFromFeatureSetID.

E

EMAILADDRESS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
END_ALL_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
Constant END_ALL_QUERYDATELONG="end-ALL_query-date-long"
END_PMC_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
Constant END_PMC_QUERYDATELONG="end-PMC_query-date-long"
END_QUAL_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
Constant END_QUAL_QUERYDATELONG="end-QUAL_query-date-long"
EntityController - Class in net.sourceforge.solexatools.webapp.controller
The controller.
EntityController() - Constructor for class net.sourceforge.solexatools.webapp.controller.EntityController
Constructor for EntityController.
entrezlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
 
entrezlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
 
entrezlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK
 
entrezlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK
 
entrezlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK
 
entryToObject(TupleInput) - Method in class com.github.seqware.queryengine.impl.tuplebinderIO.FeatureTB
entryToObject(TupleInput) - Method in class com.github.seqware.queryengine.impl.tuplebinderIO.SGIDTB
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.ConsequenceTB
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.ContigPositionTB
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.CoverageTB
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.FeatureTB
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.StringIdTB
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.TagTB
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.VariantTB
Environment - Class in net.sourceforge.seqware.pipeline.workflowV2.model
 
Environment() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
EnvUtil - Class in net.sourceforge.seqware.queryengine.webservice.util
EnvUtil class.
EnvUtil() - Constructor for class net.sourceforge.seqware.queryengine.webservice.util.EnvUtil
 
ENVVARNOTFOUND - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant ENVVARNOTFOUND=14
EOF - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant EOF=-1
EOF - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant EOF=-1
EQUALS - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant EQUALS=9
EQUALS - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant EQUALS=9
equals(Object) - Method in class com.github.seqware.queryengine.kernel.RPNStack.Parameter
 
equals(Object) - Method in class com.github.seqware.queryengine.model.Feature
equals(Object) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
equals(Object) - Method in class com.github.seqware.queryengine.model.impl.FeatureList
equals(Object) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
Override the equals method for Group, kind of a cheat With other objects we take into account things like version or SGID However, with Group, the object is embedded inside the ACL for other objects explicitly, so the version changes too often for easy API use
equals(Object) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
equals(Object) - Method in class com.github.seqware.queryengine.model.Tag
equals(Object) - Method in class com.github.seqware.queryengine.model.User
equals(Object) - Method in class com.github.seqware.queryengine.util.LazyReference
equals(Object) - Method in class com.github.seqware.queryengine.util.SGID
equals(Object) - Method in class net.sourceforge.seqware.common.model.Expense
equals(Object) - Method in class net.sourceforge.seqware.common.model.Experiment
equals(Object) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
equals(Object) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
equals(Object) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
equals(Object) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
equals(Object) - Method in class net.sourceforge.seqware.common.model.File
equals(Object) - Method in class net.sourceforge.seqware.common.model.FileType
equals(Object) - Method in class net.sourceforge.seqware.common.model.Invoice
equals(Object) - Method in class net.sourceforge.seqware.common.model.IUS
equals(Object) - Method in class net.sourceforge.seqware.common.model.Lane
equals(Object) - Method in class net.sourceforge.seqware.common.model.LibrarySelection
equals(Object) - Method in class net.sourceforge.seqware.common.model.LibrarySource
equals(Object) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
equals(Object) - Method in class net.sourceforge.seqware.common.model.Organism
equals(Object) - Method in class net.sourceforge.seqware.common.model.Platform
equals(Object) - Method in class net.sourceforge.seqware.common.model.Processing
equals(Object) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
equals(Object) - Method in class net.sourceforge.seqware.common.model.Project
equals(Object) - Method in class net.sourceforge.seqware.common.model.Registration
equals(Object) - Method in class net.sourceforge.seqware.common.model.Sample
equals(Object) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
equals(Object) - Method in class net.sourceforge.seqware.common.model.SequencerRun
equals(Object) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
equals(Object) - Method in class net.sourceforge.seqware.common.model.ShareStudy
equals(Object) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
equals(Object) - Method in class net.sourceforge.seqware.common.model.Study
equals(Object) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
equals(Object) - Method in class net.sourceforge.seqware.common.model.StudyType
equals(Object) - Method in class net.sourceforge.seqware.common.model.Workflow
equals(Object) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
equals(Object) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
equals(Object) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
equals(Object) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
equals(Object) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
equals(Object) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
equals(Object) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
 
equals(Object) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
equals(Object) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
 
error(Object) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.error(Object).
error(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.error(Object,Throwable).
evaluate() - Method in class com.github.seqware.queryengine.kernel.RPNStack
RPN evaluation.
evaluateReturn(Module, String) - Method in class net.sourceforge.seqware.pipeline.runner.Runner
evaluateReturn.
evict(Object) - Static method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions
evict.
ExceptionTools - Class in net.sourceforge.seqware.common.util.exceptiontools
ExceptionTools class.
ExceptionTools() - Constructor for class net.sourceforge.seqware.common.util.exceptiontools.ExceptionTools
 
executeQuery(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
executeQuery.
executeUpdate(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
executeUpdate.
existingStudyType - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE
 
existsExperiment(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
 
existsIUS(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
 
existsLane(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
 
existsProcessing(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
 
existsSample(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
 
existsSequencerRun(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
 
existsStudy(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
 
EXIT_CODE_EXISTING_NAME - Static variable in class com.github.seqware.queryengine.system.importers.FeatureImporter
Constant EXIT_CODE_EXISTING_NAME=5
EXIT_CODE_INVALID_ARGS - Static variable in class com.github.seqware.queryengine.system.importers.FeatureImporter
Constant EXIT_CODE_INVALID_ARGS=1
EXIT_CODE_INVALID_FILE - Static variable in class com.github.seqware.queryengine.system.importers.FeatureImporter
Constant EXIT_CODE_INVALID_FILE=10
ExitException - Exception in net.sourceforge.seqware.common.util
Created by IntelliJ IDEA.
ExitException(int) - Constructor for exception net.sourceforge.seqware.common.util.ExitException
Constructor for ExitException.
exitStatus - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
expansion(String) - Static method in class net.sourceforge.seqware.common.util.TabExpansionUtil
Produce output resembling Postgres with one "table" per record
expectedbasecall - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
 
expectedNumberReads - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
expectedNumberRuns - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
expectedNumberSpots - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
Expense - Class in net.sourceforge.seqware.common.model
Expense class.
Expense() - Constructor for class net.sourceforge.seqware.common.model.Expense
Constructor for Expense.
Experiment - Class in net.sourceforge.seqware.common.model
 
Experiment() - Constructor for class net.sourceforge.seqware.common.model.Experiment
Constructor for Experiment.
experiment - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentSet
 
EXPERIMENT_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant EXPERIMENT_ATTRIBUTES="Header.EXPERIMENT_ATTRIBUTES.getTitle()"
EXPERIMENT_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant EXPERIMENT_NAME="Header.EXPERIMENT_NAME.getTitle()"
EXPERIMENT_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
Constant EXPERIMENT_PREFIX="exp_"
EXPERIMENT_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant EXPERIMENT_SWA="Header.EXPERIMENT_SWA.getTitle()"
EXPERIMENT_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant EXPERIMENT_TAG_PREFIX="Header.EXPERIMENT_TAG_PREFIX.getTitle()"
ExperimentAttribute - Class in net.sourceforge.seqware.common.model
ExperimentAttribute generated by hbm2java
ExperimentAttribute() - Constructor for class net.sourceforge.seqware.common.model.ExperimentAttribute
Constructor for ExperimentAttribute.
ExperimentAttribute(int, Experiment) - Constructor for class net.sourceforge.seqware.common.model.ExperimentAttribute
Constructor for ExperimentAttribute.
ExperimentAttribute(int, Experiment, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.ExperimentAttribute
Constructor for ExperimentAttribute.
experimentattribute - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES
 
ExperimentAttributeDAO - Interface in net.sourceforge.seqware.common.dao
ExperimentAttributeDAO interface.
ExperimentAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ExperimentAttributeDAOHibernate class.
ExperimentAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate
 
experimentattributes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
ExperimentController - Class in net.sourceforge.solexatools.webapp.controller
ExperimentController
ExperimentController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ExperimentController
Constructor for ExperimentController.
ExperimentController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.ExperimentController
Constructor for ExperimentController.
ExperimentDAO - Interface in net.sourceforge.seqware.common.dao
ExperimentDAO interface.
ExperimentDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ExperimentDAOHibernate class.
ExperimentDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
Constructor for ExperimentDAOHibernate.
ExperimentIDFilter - Class in net.sourceforge.seqware.webservice.resources.filters
ExperimentIDFilter class.
ExperimentIDFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.ExperimentIDFilter
 
ExperimentIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
ExperimentIDResource class.
ExperimentIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ExperimentIDResource
Constructor for ExperimentIDResource.
ExperimentLibraryDesign - Class in net.sourceforge.seqware.common.model
ExperimentLibraryDesign class.
ExperimentLibraryDesign() - Constructor for class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Constructor for ExperimentLibraryDesign.
ExperimentLibraryDesignDAO - Interface in net.sourceforge.seqware.common.dao
ExperimentLibraryDesignDAO interface.
ExperimentLibraryDesignDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ExperimentLibraryDesignDAOHibernate class.
ExperimentLibraryDesignDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate
Constructor for ExperimentLibraryDesignDAOHibernate.
ExperimentLibraryDesignService - Interface in net.sourceforge.seqware.common.business
ExperimentLibraryDesignService interface.
ExperimentLibraryDesignServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ExperimentLibraryDesignServiceImpl class.
ExperimentLibraryDesignServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl
Constructor for ExperimentLibraryDesignServiceImpl.
ExperimentLink - Class in net.sourceforge.seqware.common.model
ExperimentLink generated by hbm2java
ExperimentLink() - Constructor for class net.sourceforge.seqware.common.model.ExperimentLink
Constructor for ExperimentLink.
ExperimentLink(int, Experiment) - Constructor for class net.sourceforge.seqware.common.model.ExperimentLink
Constructor for ExperimentLink.
ExperimentLink(int, Experiment, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.ExperimentLink
Constructor for ExperimentLink.
experimentlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS
 
ExperimentLinkDAO - Interface in net.sourceforge.seqware.common.dao
ExperimentLinkDAO interface.
ExperimentLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ExperimentLinkDAOHibernate class.
ExperimentLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate
 
experimentlinks - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
ExperimentList - Class in net.sourceforge.seqware.common.model.lists
ExperimentList class.
ExperimentList() - Constructor for class net.sourceforge.seqware.common.model.lists.ExperimentList
Constructor for ExperimentList.
experimentref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
 
experimentref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
ExperimentResource - Class in net.sourceforge.seqware.webservice.resources.tables
ExperimentResource class.
ExperimentResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ExperimentResource
Constructor for ExperimentResource.
ExperimentService - Interface in net.sourceforge.seqware.common.business
ExperimentService interface.
ExperimentServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ExperimentServiceImpl class.
ExperimentServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
Constructor for ExperimentServiceImpl.
ExperimentSet - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentSet() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentSet
 
ExperimentSetupController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
ExperimentSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
Constructor for ExperimentSetupController.
ExperimentSpotDesign - Class in net.sourceforge.seqware.common.model
ExperimentSpotDesign class.
ExperimentSpotDesign() - Constructor for class net.sourceforge.seqware.common.model.ExperimentSpotDesign
Constructor for ExperimentSpotDesign.
ExperimentSpotDesignDAO - Interface in net.sourceforge.seqware.common.dao
ExperimentSpotDesignDAO interface.
ExperimentSpotDesignDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ExperimentSpotDesignDAOHibernate class.
ExperimentSpotDesignDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate
Constructor for ExperimentSpotDesignDAOHibernate.
ExperimentSpotDesignReadSpec - Class in net.sourceforge.seqware.common.model
ExperimentSpotDesignReadSpec class.
ExperimentSpotDesignReadSpec() - Constructor for class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Constructor for ExperimentSpotDesignReadSpec.
ExperimentSpotDesignReadSpecComparator - Class in net.sourceforge.seqware.common.model.comparator
ExperimentSpotDesignReadSpecComparator class.
ExperimentSpotDesignReadSpecComparator() - Constructor for class net.sourceforge.seqware.common.model.comparator.ExperimentSpotDesignReadSpecComparator
 
ExperimentSpotDesignReadSpecDAO - Interface in net.sourceforge.seqware.common.dao
ExperimentSpotDesignReadSpecDAO interface.
ExperimentSpotDesignReadSpecDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ExperimentSpotDesignReadSpecDAOHibernate class.
ExperimentSpotDesignReadSpecDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate
Constructor for ExperimentSpotDesignReadSpecDAOHibernate.
ExperimentSpotDesignReadSpecService - Interface in net.sourceforge.seqware.common.business
ExperimentSpotDesignReadSpecService interface.
ExperimentSpotDesignReadSpecServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ExperimentSpotDesignReadSpecServiceImpl class.
ExperimentSpotDesignReadSpecServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl
Constructor for ExperimentSpotDesignReadSpecServiceImpl.
ExperimentSpotDesignService - Interface in net.sourceforge.seqware.common.business
ExperimentSpotDesignService interface.
ExperimentSpotDesignServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ExperimentSpotDesignServiceImpl class.
ExperimentSpotDesignServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl
Constructor for ExperimentSpotDesignServiceImpl.
ExperimentType - Class in net.sourceforge.seqware.queryengine.webservice.model
An Experiment specifies of what will be sequenced and how the sequencing will be performed.
ExperimentType() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
ExperimentType.DESIGN - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.DESIGN() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
 
ExperimentType.DESIGN.LIBRARYDESCRIPTOR - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.DESIGN.LIBRARYDESCRIPTOR() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
 
ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
 
ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
 
ExperimentType.DESIGN.SAMPLEDESCRIPTOR - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.DESIGN.SAMPLEDESCRIPTOR() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR
 
ExperimentType.DESIGN.SPOTDESCRIPTOR - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.DESIGN.SPOTDESCRIPTOR() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR
 
ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
 
ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
 
ExperimentType.EXPERIMENTATTRIBUTES - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.EXPERIMENTATTRIBUTES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES
 
ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
 
ExperimentType.EXPERIMENTLINKS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.EXPERIMENTLINKS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS
 
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
 
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
 
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
 
ExperimentType.PLATFORM - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PLATFORM() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
 
ExperimentType.PLATFORM.ABISOLID - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PLATFORM.ABISOLID() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
 
ExperimentType.PLATFORM.ABISOLID.COLORMATRIX - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PLATFORM.ABISOLID.COLORMATRIX() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX
 
ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
 
ExperimentType.PLATFORM.HELICOS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PLATFORM.HELICOS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
 
ExperimentType.PLATFORM.ILLUMINA - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PLATFORM.ILLUMINA() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
 
ExperimentType.PLATFORM.LS454 - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PLATFORM.LS454() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
 
ExperimentType.PROCESSING - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PROCESSING() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING
 
ExperimentType.PROCESSING.BASECALLS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PROCESSING.BASECALLS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS
 
ExperimentType.PROCESSING.QUALITYSCORES - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.PROCESSING.QUALITYSCORES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
 
ExperimentType.STUDYREF - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
ExperimentType.STUDYREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF
 
ExperimentUpdateValidator - Class in net.sourceforge.solexatools.validation
ExperimentUpdateValidator class.
ExperimentUpdateValidator() - Constructor for class net.sourceforge.solexatools.validation.ExperimentUpdateValidator
 
ExperimentValidator - Class in net.sourceforge.solexatools.validation
ExperimentValidator class.
ExperimentValidator() - Constructor for class net.sourceforge.solexatools.validation.ExperimentValidator
Constructor for ExperimentValidator.
EXPIRYTIME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
export() - Method in class com.github.seqware.queryengine.system.exporters.VCFDumper
export.
export() - Method in class com.github.seqware.queryengine.tutorial.BrianTest
export.
export() - Method in class com.github.seqware.queryengine.tutorial.GITest
export.
EXT_PARAMETERS - Static variable in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner
Constant EXT_PARAMETERS="ext_parameters"
ext_parameters - Variable in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner.PluginRunnerMapper
parameters that will be usable by the user (the writer of the queries)

F

Factory - Class in net.sourceforge.seqware.queryengine.backend.factory
Abstract Factory class.
Factory() - Constructor for class net.sourceforge.seqware.queryengine.backend.factory.Factory
 
FactoryInterface - Interface in net.sourceforge.seqware.queryengine.backend.factory
FactoryInterface interface.
FAILED - Static variable in class net.sourceforge.seqware.common.metadata.Metadata
Constant FAILED="failed"
FAILED - Static variable in class net.sourceforge.seqware.common.model.WorkflowRun
Constant FAILED="failed"
FAILED - Static variable in class net.sourceforge.seqware.pipeline.decider.Decider
Constant FAILED="failed"
FAILED - Static variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
Constant FAILED="failed"
FAILURE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant FAILURE=15
Fastq(File, String, String, int) - Static method in class net.sourceforge.seqware.common.util.filetools.validate.Validate
Fastq.
fastqConvNum - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
fatal(Object) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.fatal(Object).
fatal(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.fatal(Object,Throwable).
Feature - Class in com.github.seqware.queryengine.model
Features represent a GVF (which is a more generic version of a VCF).
Feature - Class in net.sourceforge.seqware.queryengine.backend.model
Feature class.
Feature() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.Feature
 
feature - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
FEATURE - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model
Constant FEATURE=30
Feature.AdditionalAttributeType - Enum in com.github.seqware.queryengine.model
 
Feature.Builder - Class in com.github.seqware.queryengine.model
 
Feature.Builder() - Constructor for class com.github.seqware.queryengine.model.Feature.Builder
 
Feature.Strand - Enum in com.github.seqware.queryengine.model
Strand locations of features.
FEATURE_SET_ID - Static variable in class com.github.seqware.queryengine.system.importers.FeatureImporter
Constant FEATURE_SET_ID="FeatureSetID"
FEATURE_SET_PARAM - Static variable in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper
Constant FEATURE_SET_PARAM='f'
FEATURE_SET_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
Constant FEATURE_SET_PARAM='f'
featureByIDRequest(String) - Method in class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
Retrieve resources.
FeatureFilter - Interface in com.github.seqware.queryengine.plugins.plugins
Interface for matching functions that we can quickly use in both in-memory and M/R plug-ins.
FeatureImporter - Class in com.github.seqware.queryengine.system.importers
Port of the class from the original prototype, adapted to use the new classes in the new API; command-line interface is the older one without support for SO.
FeatureImporter(int) - Constructor for class com.github.seqware.queryengine.system.importers.FeatureImporter
Constructor for FeatureImporter.
FeatureImporter - Class in net.sourceforge.seqware.queryengine.tools.importers
FeatureImporter class.
FeatureImporter(int) - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.FeatureImporter
Constructor for FeatureImporter.
FeatureIO - Class in com.github.seqware.queryengine.impl.protobufIO
FeatureIO class.
FeatureIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.FeatureIO
 
FeatureList - Class in com.github.seqware.queryengine.model.impl
This is an internal atom class, that should never be viewed by the user.
FeatureList() - Constructor for class com.github.seqware.queryengine.model.impl.FeatureList
Constructor for FeatureList.
FeatureList.Builder - Class in com.github.seqware.queryengine.model.impl
 
FeatureList.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.FeatureList.Builder
 
FeatureListIO - Class in com.github.seqware.queryengine.impl.protobufIO
FeatureListIO class.
FeatureListIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.FeatureListIO
 
featureNotImplemented() - Static method in class net.sourceforge.seqware.common.module.ReturnValue
featureNotImplemented.
featurePasses(Feature, Object...) - Method in interface com.github.seqware.queryengine.plugins.plugins.FeatureFilter
featurePasses.
featurePasses(Feature, Object...) - Method in class com.github.seqware.queryengine.plugins.plugins.FeaturesAllPlugin.FeaturesAllFilter
 
featurePasses(Feature, Object...) - Method in class com.github.seqware.queryengine.plugins.plugins.FeaturesByAttributesPlugin.FeaturesByAttributesFilter
 
featurePasses(Feature, Object...) - Method in class com.github.seqware.queryengine.plugins.plugins.FeaturesByRangePlugin.FeaturesByRangeFilter
 
featurePasses(Feature, Object...) - Method in class com.github.seqware.queryengine.plugins.plugins.FeaturesByTagPlugin.FeaturesByTagFilter
 
FEATURES_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
FEATURES_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
FeaturesAllPlugin - Class in com.github.seqware.queryengine.plugins.plugins
FeaturesAllPlugin class.
FeaturesAllPlugin() - Constructor for class com.github.seqware.queryengine.plugins.plugins.FeaturesAllPlugin
 
FeaturesAllPlugin.FeaturesAllFilter - Class in com.github.seqware.queryengine.plugins.plugins
 
FeaturesAllPlugin.FeaturesAllFilter() - Constructor for class com.github.seqware.queryengine.plugins.plugins.FeaturesAllPlugin.FeaturesAllFilter
 
FeaturesByAttributesPlugin - Class in com.github.seqware.queryengine.plugins.plugins
Generic query implementation over all attributes of a Feature (including additional attributes).
FeaturesByAttributesPlugin() - Constructor for class com.github.seqware.queryengine.plugins.plugins.FeaturesByAttributesPlugin
 
FeaturesByAttributesPlugin.FeaturesByAttributesFilter - Class in com.github.seqware.queryengine.plugins.plugins
 
FeaturesByAttributesPlugin.FeaturesByAttributesFilter() - Constructor for class com.github.seqware.queryengine.plugins.plugins.FeaturesByAttributesPlugin.FeaturesByAttributesFilter
 
FeaturesByFilterPlugin - Class in com.github.seqware.queryengine.plugins.plugins
Implements the generic queries which independently decide on whether a Feature is included in a result.
FeaturesByFilterPlugin() - Constructor for class com.github.seqware.queryengine.plugins.plugins.FeaturesByFilterPlugin
 
FeaturesByRangePlugin - Class in com.github.seqware.queryengine.plugins.plugins
Retrieves features based on their chromosomal location.
FeaturesByRangePlugin() - Constructor for class com.github.seqware.queryengine.plugins.plugins.FeaturesByRangePlugin
 
FeaturesByRangePlugin.FeaturesByRangeFilter - Class in com.github.seqware.queryengine.plugins.plugins
 
FeaturesByRangePlugin.FeaturesByRangeFilter() - Constructor for class com.github.seqware.queryengine.plugins.plugins.FeaturesByRangePlugin.FeaturesByRangeFilter
 
FeaturesByTagPlugin - Class in com.github.seqware.queryengine.plugins.plugins
FeaturesByTagPlugin class.
FeaturesByTagPlugin() - Constructor for class com.github.seqware.queryengine.plugins.plugins.FeaturesByTagPlugin
 
FeaturesByTagPlugin.FeaturesByTagFilter - Class in com.github.seqware.queryengine.plugins.plugins
 
FeaturesByTagPlugin.FeaturesByTagFilter() - Constructor for class com.github.seqware.queryengine.plugins.plugins.FeaturesByTagPlugin.FeaturesByTagFilter
 
FeatureSet - Class in com.github.seqware.queryengine.model
A feature set is a set (ex: collection, bag) of features.
FeatureSet() - Constructor for class com.github.seqware.queryengine.model.FeatureSet
Creates an instance of an anonymous feature set.
FeatureSet.Builder - Class in com.github.seqware.queryengine.model
 
FeatureSet.Builder() - Constructor for class com.github.seqware.queryengine.model.FeatureSet.Builder
 
FEATURESET_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
FeatureSetCountPlugin - Class in com.github.seqware.queryengine.plugins.plugins
Counts the number of Features in a FeatureSet
FeatureSetCountPlugin() - Constructor for class com.github.seqware.queryengine.plugins.plugins.FeatureSetCountPlugin
 
featureSetID - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
FEATURESETIDS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
FeatureSetIO - Class in com.github.seqware.queryengine.impl.protobufIO
FeatureSetIO class.
FeatureSetIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.FeatureSetIO
 
FeatureSetListingResource - Class in com.github.seqware.queryengine.system.rest.resources
 
FeatureSetListingResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.FeatureSetListingResource
 
FeatureSetResource - Class in com.github.seqware.queryengine.system.rest.resources
FeatureSet resource.
FeatureSetResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.FeatureSetResource
 
featureSets() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference
Get the list of feature sets associated with this reference.
featureSets() - Method in interface com.github.seqware.queryengine.model.Reference
Get the list of feature sets associated with this reference.
featuresRequest() - Method in class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
List available resources.
FeatureStoreInterface - Interface in net.sourceforge.seqware.queryengine.backend.store
FeatureStoreInterface interface.
FeatureTB - Class in com.github.seqware.queryengine.impl.tuplebinderIO
FeatureTB class.
FeatureTB() - Constructor for class com.github.seqware.queryengine.impl.tuplebinderIO.FeatureTB
 
FeatureTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders
FeatureTB class.
FeatureTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.FeatureTB
 
FIELDS - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
Constant FIELDS=2
FIELDS - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
Constant FIELDS=2
FIELDS - Static variable in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Constant FIELDS=2
fields - Variable in class net.sourceforge.seqware.webservice.resources.BasicResource
 
fields - Variable in class net.sourceforge.seqware.webservice.resources.BasicRestlet
 
fieldsConfirmed(String[]) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
File - Class in net.sourceforge.seqware.common.model
File class.
File() - Constructor for class net.sourceforge.seqware.common.model.File
Constructor for File.
file - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES
 
file - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES
 
file - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES
 
FILE_EXPERIMENT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_EXPERIMENT_NAME="f_exp_name"
FILE_EXPERIMENT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_EXPERIMENT_NAME="f_exp_name"
FILE_EXPERIMENT_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_EXPERIMENT_SWID="f_exp_swid"
FILE_EXPERIMENT_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_EXPERIMENT_SWID="f_exp_swid"
FILE_FILE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_FILE="f_file"
FILE_FILE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_FILE="f_file"
FILE_IUS - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_IUS="f_ius"
FILE_IUS - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_IUS="f_ius"
FILE_IUS_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_IUS_NAME="f_ius_name"
FILE_IUS_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_IUS_SWID="f_ius_swid"
FILE_IUS_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_IUS_SWID="f_ius_swid"
FILE_IUS_TAG - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_IUS_TAG="f_ius_tag"
FILE_IUS_TAG - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_IUS_TAG="f_ius_tag"
FILE_LANE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_LANE="f_lane"
FILE_LANE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_LANE="f_lane"
FILE_LANE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_LANE_NAME="f_lane_name"
FILE_LANE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_LANE_NAME="f_lane_name"
FILE_LANE_NUMBER - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_LANE_NUMBER="f_lane_num"
FILE_LANE_NUMBER - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_LANE_NUMBER="f_lane_num"
FILE_LANE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_LANE_SWID="f_lane_swid"
FILE_LANE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_LANE_SWID="f_lane_swid"
FILE_LIBRARY - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_LIBRARY="f_library"
FILE_LIBRARY - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_LIBRARY="f_library"
FILE_META_TYPE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_META_TYPE="f_file_meta"
FILE_META_TYPE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_META_TYPE="f_file_meta"
FILE_PARENT_SAMPLE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_PARENT_SAMPLE_NAME="f_sample_name"
FILE_PARENT_SAMPLE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_PARENT_SAMPLE_NAME="f_sample_name"
FILE_PARENT_SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_PARENT_SAMPLE_SWID="f_sample_swid"
FILE_PARENT_SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_PARENT_SAMPLE_SWID="f_sample_swid"
FILE_PATH - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_PATH="f_file_path"
FILE_PATH - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_PATH="f_file_path"
FILE_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
Constant FILE_PREFIX="fl_"
FILE_PROCESSING_ALG - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_PROCESSING_ALG="f_processing_alg"
FILE_PROCESSING_ALG - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_PROCESSING_ALG="f_processing_alg"
FILE_PROCESSING_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_PROCESSING_SWID="f_processing_swid"
FILE_PROCESSING_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_PROCESSING_SWID="f_processing_swid"
FILE_RUN_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_RUN_NAME="f_run_name"
FILE_RUN_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_RUN_NAME="f_run_name"
FILE_RUN_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_RUN_SWID="f_run_swid"
FILE_RUN_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_RUN_SWID="f_run_swid"
FILE_SAMPLE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_SAMPLE="f_sample"
FILE_SAMPLE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_SAMPLE="f_sample"
FILE_SAMPLE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_SAMPLE_NAME="f_child_sample_name"
FILE_SAMPLE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_SAMPLE_NAME="f_child_sample_name"
FILE_SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_SAMPLE_SWID="f_child_sample_swid"
FILE_SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_SAMPLE_SWID="f_child_sample_swid"
FILE_SEQUENCER_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_SEQUENCER_NAME="f_seqrun_name"
FILE_SEQUENCER_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_SEQUENCER_NAME="f_seqrun_name"
FILE_SEQUENCER_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_SEQUENCER_SWID="f_seqrun_swid"
FILE_SEQUENCER_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_SEQUENCER_SWID="f_seqrun_swid"
FILE_STUDY_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_STUDY_SWID="f_study_swid"
FILE_STUDY_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_STUDY_SWID="f_study_swid"
FILE_STUDY_TITLE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_STUDY_TITLE="f_study_title"
FILE_STUDY_TITLE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_STUDY_TITLE="f_study_title"
FILE_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant FILE_SWA="Header.FILE_SWA.getTitle()"
FILE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_SWID="f_file_swid"
FILE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_SWID="f_file_swid"
FILE_TEMPLATE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_TEMPLATE="f_template"
FILE_TEMPLATE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_TEMPLATE="f_template"
FILE_TISSUE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_TISSUE="f_tissue"
FILE_TISSUE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_TISSUE="f_tissue"
FILE_WF_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_WF_NAME="f_wf_name"
FILE_WF_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_WF_NAME="f_wf_name"
FILE_WF_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_WF_SWID="f_wf_swid"
FILE_WF_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_WF_SWID="f_wf_swid"
FILE_WF_VERSION - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant FILE_WF_VERSION="f_wf_version"
FILE_WF_VERSION - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant FILE_WF_VERSION="f_wf_version"
FileAttribute - Class in net.sourceforge.seqware.common.model
 
FileAttribute() - Constructor for class net.sourceforge.seqware.common.model.FileAttribute
Constructor for FileAttribute.
FileAttribute(Integer) - Constructor for class net.sourceforge.seqware.common.model.FileAttribute
Constructor for FileAttribute.
FileAttributeDAO - Interface in net.sourceforge.seqware.common.dao
FileAttributeDAO interface.
FileAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
FileAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
 
FileAttributeResource - Interface in net.sourceforge.seqware.webservice.resources.tables
FileAttributeResource interface.
FileAttributeServerResource - Class in net.sourceforge.seqware.webservice.resources.tables
FileAttributeServerResource class.
FileAttributeServerResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource
Constructor for FileAttributeServerResource.
FileAttributeService - Interface in net.sourceforge.seqware.common.business
FileAttributeService interface.
FileAttributeServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
FileAttributeServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl
 
FileAttributesResource - Interface in net.sourceforge.seqware.webservice.resources.tables
FileAttributesResource interface.
FileAttributesServerResource - Class in net.sourceforge.seqware.webservice.resources.tables
FileAttributesServerResource class.
FileAttributesServerResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileAttributesServerResource
Constructor for FileAttributesServerResource.
FileChildWorkflowRunsResource - Class in net.sourceforge.seqware.webservice.resources.tables
This resource will pull back the workflow runs that are generated from a particular file.
FileChildWorkflowRunsResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource
Constructor for FileChildWorkflowRunsResource.
FileChildWorkflowRunsResource.SEARCH_TYPE - Enum in net.sourceforge.seqware.webservice.resources.tables
 
FileController - Class in net.sourceforge.solexatools.webapp.controller
LaneController
FileController() - Constructor for class net.sourceforge.solexatools.webapp.controller.FileController
Constructor for FileController.
FileController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.FileController
Constructor for FileController.
FileDAO - Interface in net.sourceforge.seqware.common.dao
FileDAO interface.
FileDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
FileDAOHibernate class.
FileDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
Constructor for FileDAOHibernate.
FileDto - Class in net.sourceforge.seqware.webservice.dto
 
FileDto() - Constructor for class net.sourceforge.seqware.webservice.dto.FileDto
 
FILEEMPTY - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant FILEEMPTY=12
fileExistsAndExecutable(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
fileExistsAndExecutable.
fileExistsAndNotEmpty(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
fileExistsAndNotEmpty.
fileExistsAndReadable(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
fileExistsAndReadable.
FileFinder - Class in net.sourceforge.solexatools.util
FileFinder class.
FileFinder() - Constructor for class net.sourceforge.solexatools.util.FileFinder
Constructor for FileFinder.
FileFinder(Pattern) - Constructor for class net.sourceforge.solexatools.util.FileFinder
Constructor for FileFinder.
FileIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
FileIDResource class.
FileIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileIDResource
Constructor for FileIDResource.
FileLinker - Class in net.sourceforge.seqware.pipeline.plugins
FileLinker class.
FileLinker() - Constructor for class net.sourceforge.seqware.pipeline.plugins.FileLinker
 
FileLinkerLine - Class in net.sourceforge.seqware.pipeline.plugins.filelinker
 
FileLinkerLine() - Constructor for class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
FileLinkerLineException - Exception in net.sourceforge.seqware.pipeline.plugins.filelinker
 
FileLinkerLineException(String) - Constructor for exception net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLineException
 
FileLinkerParser - Class in net.sourceforge.seqware.pipeline.plugins.filelinker
 
FileLinkerParser() - Constructor for class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerParser
 
fileLinkReport() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl
Runs the ValidationReportService.fileLinkReport(List) including all files in the SeqWare meta db.
fileLinkReport(List<Integer>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl
Every file must be associated with at least one processing node and this node in turn must be linked (either directly or through a parent) to one of the following: sequencer_run, lane, ius, sample, experiment or study.
fileLinkReport() - Method in interface net.sourceforge.seqware.common.business.ValidationReportService
Runs the ValidationReportService.fileLinkReport(List) including all files in the SeqWare meta db.
fileLinkReport(List<Integer>) - Method in interface net.sourceforge.seqware.common.business.ValidationReportService
Every file must be associated with at least one processing node and this node in turn must be linked (either directly or through a parent) to one of the following: sequencer_run, lane, ius, sample, experiment or study.
FileLinkReportResource - Class in net.sourceforge.seqware.webservice.resources.tables
FileLinkReportResource class.
FileLinkReportResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileLinkReportResource
Constructor for FileLinkReportResource.
FileList - Class in net.sourceforge.seqware.common.model.lists
FileList class.
FileList() - Constructor for class net.sourceforge.seqware.common.model.lists.FileList
Constructor for FileList.
FileMetadata - Class in net.sourceforge.seqware.common.module
This is a simple data structure to represent a file and it's metadata.
FileMetadata() - Constructor for class net.sourceforge.seqware.common.module.FileMetadata
 
FileMetadata(String, String) - Constructor for class net.sourceforge.seqware.common.module.FileMetadata
 
FileMetadata(String, String, String, String) - Constructor for class net.sourceforge.seqware.common.module.FileMetadata
 
fileName - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
fileName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
fileName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
fileName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
fileName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
filename - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE
 
filename - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE
 
filename - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
 
FILENOTEXECUTABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant FILENOTEXECUTABLE=10
FILENOTREADABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant FILENOTREADABLE=4
FILENOTWRITABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant FILENOTWRITABLE=5
FileReportDAO - Interface in net.sourceforge.seqware.common.dao
FileReportDAO interface.
FileReportDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
FileReportDAOHibernate class.
FileReportDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
 
FileReportRow - Class in net.sourceforge.seqware.common.model
FileReportRow class.
FileReportRow() - Constructor for class net.sourceforge.seqware.common.model.FileReportRow
 
FileReportService - Interface in net.sourceforge.seqware.common.business
FileReportService interface.
FileReportServiceImpl - Class in net.sourceforge.seqware.common.business.impl
FileReportServiceImpl class.
FileReportServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
 
FileResource - Class in net.sourceforge.seqware.queryengine.webservice.view
FileResource class.
FileResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.FileResource
 
FileResource - Class in net.sourceforge.seqware.webservice.resources.tables
FileResource class.
FileResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileResource
Constructor for FileResource.
fileReverseHierarchyDisplay(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl
Produces a text representation of a reverse hierarchy tree starting at a file (indicated by the provided fileSwa).
fileReverseHierarchyDisplay(Integer) - Method in interface net.sourceforge.seqware.common.business.ValidationReportService
Produces a text representation of a reverse hierarchy tree starting at a file (indicated by the provided fileSwa).
FileReverseHierarchyDisplayResource - Class in net.sourceforge.seqware.webservice.resources.tables
FileReverseHierarchyDisplayResource class.
FileReverseHierarchyDisplayResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileReverseHierarchyDisplayResource
Constructor for FileReverseHierarchyDisplayResource.
files - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
files - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
 
files - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
filesArray - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
filesArray - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
FileService - Interface in net.sourceforge.seqware.common.business
FileService interface.
FileServiceImpl - Class in net.sourceforge.seqware.common.business.impl
FileServiceImpl class.
FileServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileServiceImpl
Constructor for FileServiceImpl.
FileSetupController - Class in net.sourceforge.solexatools.webapp.controller
FileSetupController class.
FileSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.FileSetupController
 
filesFromExperiment(Experiment, Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
FIXME: notice processings directly attached to study aren't examined!
filesFromIUS(IUS, Experiment, Sample, Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
filesFromIUS.
filesFromLane(Lane, Experiment, Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
filesFromLane.
filesFromSample(Sample, Experiment, Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
filesFromSample.
filesFromStudy(Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
FIXME: notice processings directly attached to study aren't examined!
filesFromStudy(Study) - Method in class net.sourceforge.seqware.common.hibernate.PropagateOwnership
filesFromStudy.
FileTools - Class in net.sourceforge.seqware.common.util.filetools
FileTools class.
FileTools() - Constructor for class net.sourceforge.seqware.common.util.filetools.FileTools
 
FileTools.LocalhostPair - Class in net.sourceforge.seqware.common.util.filetools
 
FileTools.LocalhostPair(String, ReturnValue) - Constructor for class net.sourceforge.seqware.common.util.filetools.FileTools.LocalhostPair
 
FileType - Class in net.sourceforge.seqware.common.model
FileType class.
FileType() - Constructor for class net.sourceforge.seqware.common.model.FileType
Constructor for FileType.
filetype - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE
 
filetype - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE
 
FILETYPE_ALL - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant FILETYPE_ALL="all"
FileTypeDAO - Interface in net.sourceforge.seqware.common.dao
FileTypeDAO interface.
FileTypeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
FileTypeDAOHibernate class.
FileTypeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.FileTypeDAOHibernate
Constructor for FileTypeDAOHibernate.
FileTypeService - Interface in net.sourceforge.seqware.common.business
FileTypeService interface.
FileTypeServiceImpl - Class in net.sourceforge.seqware.common.business.impl
FileTypeServiceImpl class.
FileTypeServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl
Constructor for FileTypeServiceImpl.
FileUploadService - Interface in net.sourceforge.seqware.common.business
FileUploadService interface.
FileUploadServiceImpl - Class in net.sourceforge.seqware.common.business.impl
FileUploadServiceImpl class.
FileUploadServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
Constructor for FileUploadServiceImpl.
FileValidator - Class in net.sourceforge.solexatools.validation
FileValidator class.
FileValidator() - Constructor for class net.sourceforge.solexatools.validation.FileValidator
Constructor for FileValidator.
fillWorkflowProcessingMap(Processing, Map<WorkflowRun, Set<Processing>>) - Static method in class net.sourceforge.solexatools.util.ControllerUtil
fillWorkflowProcessingMap.
fillWorkflowProcessingMap(Processing, Map<WorkflowRun, Set<Processing>>) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
fillWorkflowProcessingMap.
filter() - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
 
filter() - Method in interface com.github.seqware.queryengine.plugins.PluginInterface
filter.
FilteredExperimentResource - Class in net.sourceforge.seqware.webservice.resources.filters
FilteredExperimentResource class.
FilteredExperimentResource() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.FilteredExperimentResource
 
filterFiles() - Method in class net.sourceforge.seqware.pipeline.decider.Decider
filterFiles.
filterInit() - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
 
filterInit() - Method in interface com.github.seqware.queryengine.plugins.PluginInterface
filterInit.
filterReturnValues(List<ReturnValue>, String, String, boolean, boolean, boolean) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
filterReturnValues.
finalize() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterable
 
find(String, Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
find.
find(String, Integer, String) - Method in interface net.sourceforge.seqware.common.business.IUSService
find.
find(String, Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
find.
find(String, Integer, String) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
find.
findAll(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO
findAll.
findAll(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO
findAll.
findAll(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate
findAll.
findAll(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate
findAll.
findAll(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate
findAll.
findAll(IUS) - Method in interface net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAO
findAll.
findAll(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate
findAll.
findAll(Lane) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAO
findAll.
findAll(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate
findAll.
findAll(Lane) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAO
findAll.
findAll(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate
findAll.
findAll(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate
findAll.
findAll(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate
findAll.
findAll(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate
findAll.
findAll(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate
findAll.
findAll(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate
findAll.
findAll(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO
findAll.
findAll(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO
findAll.
findAll(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO
findAll.
findAll(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO
findAll.
findAll(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO
findAll.
findAll(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO
findAll.
findAll(String) - Method in class net.sourceforge.solexatools.util.FileFinder
findAll.
findAll(String, String) - Method in class net.sourceforge.solexatools.util.FileFinder
findAll.
FindAllTheFiles - Class in net.sourceforge.seqware.common.hibernate
Should only be used for one query and then discarded and re-instantiated.
FindAllTheFiles() - Constructor for class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
FindAllTheFiles.Header - Enum in net.sourceforge.seqware.common.hibernate
 
findBelongsToStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
findBelongsToStudy.
findBelongsToStudy(Study) - Method in interface net.sourceforge.seqware.common.business.IUSService
findBelongsToStudy.
findBelongsToStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
findBelongsToStudy.
findBelongsToStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
findBelongsToStudy.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.FileService
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
findByCriteria.
findByCriteria(String) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.IUSService
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.LaneService
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.SampleService
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
findByCriteria.
findByCriteria(String) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
findByCriteria.
findByCriteria(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
findByCriteria.
findByCriteria(String) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
findByCriteria.
findByEmailAddress(String) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
findByEmailAddress.
findByEmailAddress(String) - Method in interface net.sourceforge.seqware.common.business.RegistrationService
findByEmailAddress.
findByEmailAddress(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate
findByEmailAddress.
findByEmailAddress(String) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO
findByEmailAddress.
findByEmailAddressAndPassword(String, String) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
findByEmailAddressAndPassword.
findByEmailAddressAndPassword(String, String) - Method in interface net.sourceforge.seqware.common.business.RegistrationService
findByEmailAddressAndPassword.
findByEmailAddressAndPassword(String, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate
findByEmailAddressAndPassword.
findByEmailAddressAndPassword(String, String) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO
findByEmailAddressAndPassword.
findByFilePath(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
findByFilePath.
findByFilePath(String) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
findByFilePath.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.FileService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.FileTypeService
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
findByID.
findById(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleSearchServiceImpl
findById.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.OrganismService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.PlatformService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ProjectService
findByID.
findById(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleSearchService
findById.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareFileService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileTypeDAO
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileTypeDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
findByID.
findById(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleSearchDAOHibernate
findById.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LibrarySelectionDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LibrarySourceDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LibraryStrategyDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.OrganismDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.PlatformDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
findByID.
findById(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleSearchDAO
findById.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
findByID.
findByIDOnlyWithRunningWR(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
findByIDOnlyWithRunningWR.
findByIDOnlyWithRunningWR(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
findByIDOnlyWithRunningWR.
findByIDWithIUS(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
findByIDWithIUS.
findByIDWithIUS(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
findByIDWithIUS.
findByIDWithIUSAndRunningWR(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
findByIDWithIUSAndRunningWR.
findByIDWithIUSAndRunningWR(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
findByIDWithIUSAndRunningWR.
findByIDWithParams(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
findByIDWithParams.
findByIDWithParams(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
findByIDWithParams.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.business.LaneService
findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.business.ProjectService
findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.business.SampleService
findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService
findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate
findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate
findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO
findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO
findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
findByName.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
findByOwnerID.
findByOwnerId(Integer) - Method in interface net.sourceforge.seqware.common.business.FileService
findByOwnerId.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
findByOwnerID.
findByOwnerId(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
findByOwnerId.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareFileService
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
findByOwnerID.
findByOwnerId(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
findByOwnerId.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
findByOwnerID.
findByOwnerId(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
findByOwnerId.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
findByOwnerID.
findByPath(String) - Method in interface net.sourceforge.seqware.common.business.FileService
findByPath.
findByPath(String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
findByPath.
findByPath(String) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
findByPath.
findByPath(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
findByPath.
findByProcessingExperiment(Processing, Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
findByProcessingExperiment.
findByProcessingExperiment(Processing, Experiment) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService
findByProcessingExperiment.
findByProcessingExperiment(Processing, Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate
findByProcessingExperiment.
findByProcessingExperiment(Processing, Experiment) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO
findByProcessingExperiment.
findByProcessingIUS(Processing, IUS) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
findByProcessingIUS.
findByProcessingIUS(Processing, IUS) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService
findByProcessingIUS.
findByProcessingIUS(Processing, IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate
findByProcessingIUS.
findByProcessingIUS(Processing, IUS) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO
findByProcessingIUS.
findByProcessingLane(Processing, Lane) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
findByProcessingLane.
findByProcessingLane(Processing, Lane) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService
findByProcessingLane.
findByProcessingLane(Processing, Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate
findByProcessingLane.
findByProcessingLane(Processing, Lane) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO
findByProcessingLane.
findByProcessings(Processing, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
findByProcessings.
findByProcessings(Processing, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService
findByProcessings.
findByProcessings(Processing, Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate
findByProcessings.
findByProcessings(Processing, Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO
findByProcessings.
findByProcessingSample(Processing, Sample) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
findByProcessingSample.
findByProcessingSample(Processing, Sample) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService
findByProcessingSample.
findByProcessingSample(Processing, Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate
findByProcessingSample.
findByProcessingSample(Processing, Sample) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO
findByProcessingSample.
findByProcessingSequencerRun(Processing, SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
findByProcessingSequencerRun.
findByProcessingSequencerRun(Processing, SequencerRun) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService
findByProcessingSequencerRun.
findByProcessingSequencerRun(Processing, SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate
findByProcessingSequencerRun.
findByProcessingSequencerRun(Processing, SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO
findByProcessingSequencerRun.
findByProcessingStudy(Processing, Study) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
findByProcessingStudy.
findByProcessingStudy(Processing, Study) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService
findByProcessingStudy.
findByProcessingStudy(Processing, Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate
findByProcessingStudy.
findByProcessingStudy(Processing, Study) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO
findByProcessingStudy.
findByStudyIdAndRegistrationId(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
findByStudyIdAndRegistrationId.
findByStudyIdAndRegistrationId(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
findByStudyIdAndRegistrationId.
findByStudyIdAndRegistrationId(Integer, Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate
findByStudyIdAndRegistrationId.
findByStudyIdAndRegistrationId(Integer, Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO
findByStudyIdAndRegistrationId.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.FileService
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
findBySWAccession.
findBySWAccession(Long) - Method in class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl
Returns library matching given SeqWare Accession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService
findBySWAccession.
findBySWAccession(Long) - Method in interface net.sourceforge.seqware.common.business.LibraryService
Returns library matching given SeqWare Accession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareFileService
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
findBySWAccession.
findBySWAccession(Long) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate
Returns library matching given SeqWare Accesssion.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
findBySWAccession.
findBySWAccession(Long) - Method in interface net.sourceforge.seqware.common.dao.LibraryDAO
Returns library matching given SeqWare Accesssion.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
findBySWAccession.
findByTitle(String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
findByTitle.
findByTitle(String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
findByTitle.
findByTitle(String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
findByTitle.
findByTitle(String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
findByTitle.
findByTitle(String) - Method in interface net.sourceforge.seqware.common.business.SampleService
findByTitle.
findByTitle(String) - Method in interface net.sourceforge.seqware.common.business.StudyService
findByTitle.
findByTitle(String) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
findByTitle.
findByTitle(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
findByTitle.
findByTitle(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
findByTitle.
findByTitle(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
findByTitle.
findByTitle(String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
findByTitle.
findByTitle(String) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
findByTitle.
findByWorkflowRunIdAndRegistrationId(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
findByWorkflowRunIdAndRegistrationId.
findByWorkflowRunIdAndRegistrationId(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
findByWorkflowRunIdAndRegistrationId.
findByWorkflowRunIdAndRegistrationId(Integer, Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
findByWorkflowRunIdAndRegistrationId.
findByWorkflowRunIdAndRegistrationId(Integer, Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
findByWorkflowRunIdAndRegistrationId.
FindChildUtil - Class in net.sourceforge.solexatools.util
FindChildUtil class.
FindChildUtil() - Constructor for class net.sourceforge.solexatools.util.FindChildUtil
 
findDirectories(String) - Method in class net.sourceforge.solexatools.util.FileFinder
findDirectories.
findDirectories(String, String) - Method in class net.sourceforge.solexatools.util.FileFinder
findDirectories.
findFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
findFiles.
findFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
findFiles.
findFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
findFiles.
findFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
findFiles.
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService
findFiles.
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService
findFiles.
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService
findFiles.
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
findFiles.
findFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
findFiles.
findFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
findFiles.
findFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
findFiles.
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
findFiles.
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
findFiles.
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
findFiles.
findFiles(Collection<Processing>) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
 
findFiles(String) - Method in class net.sourceforge.solexatools.util.FileFinder
findFiles.
findFiles(String, String) - Method in class net.sourceforge.solexatools.util.FileFinder
findFiles.
findFilesAssociatedWithASample(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
findFilesAssociatedWithASample.
findFilesAssociatedWithASample(String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
findFilesAssociatedWithASample(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
findFilesAssociatedWithASample.
findFilesAssociatedWithASample(String, boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
findFilesAssociatedWithASample.
findFilesAssociatedWithASample(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
findFilesAssociatedWithASample.
findFilesAssociatedWithASample(String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
findFilesAssociatedWithASample(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
findFilesAssociatedWithASample.
findFilesAssociatedWithASample(String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
findFilesAssociatedWithASequencerRun(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
findFilesAssociatedWithASequencerRun.
findFilesAssociatedWithASequencerRun(String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
findFilesAssociatedWithASequencerRun(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
findFilesAssociatedWithASequencerRun.
findFilesAssociatedWithASequencerRun(String, boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
findFilesAssociatedWithASequencerRun.
findFilesAssociatedWithASequencerRun(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
findFilesAssociatedWithASequencerRun.
findFilesAssociatedWithASequencerRun(String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
findFilesAssociatedWithASequencerRun(String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
findFilesAssociatedWithASequencerRun(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
findFilesAssociatedWithASequencerRun.
findFilesAssociatedWithAStudy(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
findFilesAssociatedWithAStudy.
findFilesAssociatedWithAStudy(String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
findFilesAssociatedWithAStudy(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
findFilesAssociatedWithAStudy.
findFilesAssociatedWithAStudy(String, boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
Somewhat misnamed for now, this can return a mix of files and bare-nodes in the database hierarchy resulting from FileAllTheFiles.requireFiles=false
findFilesAssociatedWithAStudy(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
findFilesAssociatedWithAStudy.
findFilesAssociatedWithAStudy(String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
findFilesAssociatedWithAStudy(String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
findFilesAssociatedWithAStudy(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
findFilesAssociatedWithAStudy.
findFirstWorkflowClass(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowClassFinder
find the first .class in the clazzPath This has been modified to locate a specific class.
findFor(Sample, WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
findFor.
findFor(Sample) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
findFor.
findFor(Sample, WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
findFor.
findFor(Sample) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
findFor.
findIus() - Method in interface net.sourceforge.seqware.webservice.resources.tables.IusSearchResource
Locate IUS by sequencer run name, lane number and optionally sample name.
findIus() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusSearchServerResource
Locate IUS by sequencer run name, lane number and optionally sample name.
findParents(Collection<Processing>, int) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
 
FindRootUtil - Class in net.sourceforge.solexatools.util
FindRootUtil class.
FindRootUtil() - Constructor for class net.sourceforge.solexatools.util.FindRootUtil
 
findRunsForIUS(IUS) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
findRunsForIUS.
findRunsForIUS(IUS) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
findRunsForIUS.
findRunsForIUS(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
findRunsForIUS.
findRunsForIUS(IUS) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
findRunsForIUS.
findRunsForSample(Sample) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
Find all the workflow runs for the specific sample.
findRunsForSample(Sample) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
Find all the workflow runs for the specific sample.
findValueByID(WorkflowParam, Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
findValueByID.
FINISHED - Static variable in class net.sourceforge.seqware.common.model.WorkflowRun
Constant FINISHED="completed"
finishTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
finishTransaction.
finishTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
finishTransaction.
finishTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
finishTransaction.
finishTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
finishTransaction.
finishTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
finishTransaction.
FIRSTNAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
fix_file_paths(String, ArrayList<String>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
fix_file_paths.
fix_file_paths(String, ArrayList<String>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
fix_file_paths.
fix_file_paths(String, ArrayList<String>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
fix_file_paths.
fix_file_paths(String, ArrayList<String>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
fix_file_paths.
Flexigrid - Class in net.sourceforge.solexatools.webapp.metamodel
Flexigrid class.
Flexigrid(int, int) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
Constructor for Flexigrid.
Flexigrid(int) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
Constructor for Flexigrid.
Flexigrid() - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
Constructor for Flexigrid.
Flexigrid.Cells - Class in net.sourceforge.solexatools.webapp.metamodel
 
Flexigrid.Cells(List<String>) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.Cells
 
Flexigrid.ColumnModel - Class in net.sourceforge.solexatools.webapp.metamodel
 
Flexigrid.ColumnModel(String, String, int, boolean, String) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
FLOAT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant FLOAT=10
FLOAT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FLOAT=10
flowcount - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
 
flowcount - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
 
flowsequence - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
 
flowsequence - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
 
flush() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Save all managed models to the back-end
flush(boolean) - Method in class com.github.seqware.queryengine.impl.HBaseModelManager
Normally, when doing a flush, we want to maintain the state of objects that
flush() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Save all managed models to the back-end
flush(boolean) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Normally, when doing a flush, we want to maintain the state of objects that
flush() - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter
 
flushObjects(List<Map.Entry<String, SimpleModelManager.AtomStatePair>>) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Flush objects to the back-end giving a working list
FOLLOW_26_in_key_value_function293 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_26_in_key_value_function293
FOLLOW_26_in_three_param_predicate342 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_26_in_three_param_predicate342
FOLLOW_26_in_three_param_predicate346 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_26_in_three_param_predicate346
FOLLOW_26_in_two_param_predicate317 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_26_in_two_param_predicate317
FOLLOW_AND_in_high_precedence_constraint117 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_AND_in_high_precedence_constraint117
FOLLOW_BRACKET_CLOSE_in_key_value_function297 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_BRACKET_CLOSE_in_key_value_function297
FOLLOW_BRACKET_CLOSE_in_nested_constraint145 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_BRACKET_CLOSE_in_nested_constraint145
FOLLOW_BRACKET_CLOSE_in_three_param_predicate350 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_BRACKET_CLOSE_in_three_param_predicate350
FOLLOW_BRACKET_CLOSE_in_two_param_predicate321 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_BRACKET_CLOSE_in_two_param_predicate321
FOLLOW_BRACKET_OPEN_in_key_value_function288 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_BRACKET_OPEN_in_key_value_function288
FOLLOW_BRACKET_OPEN_in_nested_constraint140 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_BRACKET_OPEN_in_nested_constraint140
FOLLOW_BRACKET_OPEN_in_three_param_predicate337 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_BRACKET_OPEN_in_three_param_predicate337
FOLLOW_BRACKET_OPEN_in_two_param_predicate312 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_BRACKET_OPEN_in_two_param_predicate312
FOLLOW_comparison_in_constraint165 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_comparison_in_constraint165
FOLLOW_comparison_in_constraint175 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_comparison_in_constraint175
FOLLOW_constant_in_constraint168 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_constant_in_constraint168
FOLLOW_constant_in_constraint173 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_constant_in_constraint173
FOLLOW_constraint_in_nested_constraint151 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_constraint_in_nested_constraint151
FOLLOW_EOF_in_query78 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_EOF_in_query78
FOLLOW_high_precedence_constraint_in_low_precedence_constraint91 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_high_precedence_constraint_in_low_precedence_constraint91
FOLLOW_high_precedence_constraint_in_low_precedence_constraint98 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_high_precedence_constraint_in_low_precedence_constraint98
FOLLOW_ID_in_identifier200 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_ID_in_identifier200
FOLLOW_identifier_in_constraint163 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_identifier_in_constraint163
FOLLOW_identifier_in_constraint178 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_identifier_in_constraint178
FOLLOW_key_value_function_in_identifier206 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_key_value_function_in_identifier206
FOLLOW_literal_in_constant249 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_literal_in_constant249
FOLLOW_literal_in_key_value_function291 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_literal_in_key_value_function291
FOLLOW_literal_in_key_value_function295 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_literal_in_key_value_function295
FOLLOW_literal_in_three_param_predicate340 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_literal_in_three_param_predicate340
FOLLOW_literal_in_three_param_predicate344 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_literal_in_three_param_predicate344
FOLLOW_literal_in_three_param_predicate348 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_literal_in_three_param_predicate348
FOLLOW_literal_in_two_param_predicate315 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_literal_in_two_param_predicate315
FOLLOW_literal_in_two_param_predicate319 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_literal_in_two_param_predicate319
FOLLOW_low_precedence_constraint_in_nested_constraint143 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_low_precedence_constraint_in_nested_constraint143
FOLLOW_low_precedence_constraint_in_query75 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_low_precedence_constraint_in_query75
FOLLOW_NAMED_CONSTANT_in_constant254 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_NAMED_CONSTANT_in_constant254
FOLLOW_NAMED_FUNCTION_in_key_value_function285 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_NAMED_FUNCTION_in_key_value_function285
FOLLOW_NAMED_THREE_PARAM_PREDICATE_in_three_param_predicate334 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_NAMED_THREE_PARAM_PREDICATE_in_three_param_predicate334
FOLLOW_NAMED_TWO_PARAM_PREDICATE_in_two_param_predicate309 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_NAMED_TWO_PARAM_PREDICATE_in_two_param_predicate309
FOLLOW_nested_constraint_in_high_precedence_constraint113 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_nested_constraint_in_high_precedence_constraint113
FOLLOW_nested_constraint_in_high_precedence_constraint120 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_nested_constraint_in_high_precedence_constraint120
FOLLOW_NOT_in_nested_constraint135 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_NOT_in_nested_constraint135
FOLLOW_OR_in_low_precedence_constraint95 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_OR_in_low_precedence_constraint95
FOLLOW_three_param_predicate_in_constraint189 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_three_param_predicate_in_constraint189
FOLLOW_two_param_predicate_in_constraint183 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant FOLLOW_two_param_predicate_in_constraint183
FORCE_HOST - Static variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
 
FOREVER - Static variable in interface com.github.seqware.queryengine.model.interfaces.TTLable
A time to set that means that the associated object should never expire
forJSON(String) - Static method in class net.sourceforge.seqware.common.util.jsontools.JsonUtil
forJSON.
forJSON(String) - Static method in class net.sourceforge.solexatools.util.ModelUtil
forJSON.
format(String, Object...) - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter
 
format(Map<String, ? extends OptionDescriptor>) - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin.MarkDownFormatter
 
formatCode - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
 
frame - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
Freemarker - Class in net.sourceforge.seqware.common.util.freemarker
Freemarker class.
Freemarker() - Constructor for class net.sourceforge.seqware.common.util.freemarker.Freemarker
 
FREEMARKEREXCEPTION - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant FREEMARKEREXCEPTION=70
FRIENDLY_ROWKEY_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
friendlyRowKey - Variable in class com.github.seqware.queryengine.util.SGID
this can be used to override the randomly generated IDs for the back-end.
fromBaseN(String, int) - Static method in class com.github.seqware.queryengine.kernel.Compression
Returns the integer extracted from the given string in a certain base.
fromDto(AttributeDto, Class<T>) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
fromDto.
fromWorkflow(Integer) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowReport
fromWorkflow.
FSGID - Class in com.github.seqware.queryengine.util
Special class for Features which also stores the row key for features.
FSGID(long, long, long, String, String, SGID, boolean) - Constructor for class com.github.seqware.queryengine.util.FSGID
Create a fully functional FSGID given raw data
FSGID(SGID, FSGID) - Constructor for class com.github.seqware.queryengine.util.FSGID
construct a FSGID based on all the components of a SGID while taking the non-unique aspects on a FSGID, used when creating FeatureLists only
FSGID(SGID, Feature, FeatureSet) - Constructor for class com.github.seqware.queryengine.util.FSGID
Create a fully functional FSGID given models from the front-end
FSGIDIO - Class in com.github.seqware.queryengine.impl.protobufIO
FSGIDIO class.
FSGIDIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.FSGIDIO
 
fuzzyStartPositionMax - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
fuzzyStopPositionMin - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 

G

geneChr - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
geneId - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
geneId - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
generateDax(AbstractWorkflowDataModel, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.DaxgeneratorV2
generate a dax file from the object model
generateDaxFile(WorkflowInfo, File, String, Map<String, String>, List<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
generateDaxFile.
generateStatus(int) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
generateWorkflowXml(AbstractWorkflowDataModel, String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowXmlGenerator
generate a dax file from the object model
GeneReportResource - Class in net.sourceforge.seqware.queryengine.webservice.view
GeneReportResource class.
GeneReportResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.GeneReportResource
 
GenericCommandRunner - Class in net.sourceforge.seqware.pipeline.modules
This is a very simple module that takes a few options on the command line and then passes the rest of the arguments to whatever command is specified.
GenericCommandRunner() - Constructor for class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
 
GenericDBResource - Class in net.sourceforge.seqware.webservice.resources.queries
GenericDBResource class.
GenericDBResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.GenericDBResource
Constructor for GenericDBResource.
GenericElementResource<T extends Atom> - Class in com.github.seqware.queryengine.system.rest.resources
Describes the basic operations that we wish to define on elements (which may or may not be found inside sets).
GenericElementResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
 
GenericMetadataSaver - Class in net.sourceforge.seqware.pipeline.modules
This is a very simple module is used to save both a processing event and 0 or more files to the metadb.
GenericMetadataSaver() - Constructor for class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
 
GenericMutableSetResource<T extends Atom> - Class in com.github.seqware.queryengine.system.rest.resources
 
GenericMutableSetResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.GenericMutableSetResource
 
GenericSetResource<T extends Atom> - Class in com.github.seqware.queryengine.system.rest.resources
 
GenericSetResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.GenericSetResource
 
GenericTemplateResource - Class in net.sourceforge.seqware.queryengine.webservice.view
GenericTemplateResource class.
GenericTemplateResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
genomeId - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
genomeTable - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
genomicSequence - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
get(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
get.
get() - Method in class com.github.seqware.queryengine.model.PluginRun
Blocking call to retrieve results of a query
get() - Method in interface com.github.seqware.queryengine.model.QueryFuture
Blocking call to retrieve results of a query
get(String) - Method in interface com.github.seqware.queryengine.model.TagSet
get.
get() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner
 
get() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryPluginRunner
 
get() - Method in interface com.github.seqware.queryengine.plugins.PluginRunnerInterface
 
get() - Method in class com.github.seqware.queryengine.util.LazyLatestReference
Retrieve the lazy referenced object if possible and return it
get() - Method in class com.github.seqware.queryengine.util.LazyReference
Retrieve the lazy referenced object if possible and return it
get(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService
get.
get(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl
get.
get(File) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO
get.
get(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO
get.
get(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
get.
get(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
get.
get(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
get.
get(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
get.
get(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
get.
get(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
get.
get(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
get.
get(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
get.
get(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
get.
get(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
get.
get() - Static method in class net.sourceforge.seqware.common.factory.DBAccess
get.
get(String, String, boolean) - Method in class net.sourceforge.seqware.pipeline.runner.RunnerParams
get.
get() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunIDsFilter
get() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter
get() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
get() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionResource
get() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource
get_description() - Method in class net.sourceforge.seqware.pipeline.decider.Decider
Generates a short description of the plugin, preferably one line.
get_description() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
Generates a short description of the plugin, preferably one line.
get_description() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
 
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator
Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection
Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager
get_description.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker
Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker
 
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
get_description.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
get_description.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner
get_description.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.OozieXML2Dot
 
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot
 
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter
Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter
Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter
Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
Generates a short description of the plugin, preferably one line.
get_galaxy_xml() - Method in class net.sourceforge.seqware.pipeline.module.Module
Output Galaxy definition files so you can use this module with Galaxy.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.decider.Decider
Generates a "help" message for the user of the plugin.
get_syntax() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Generates a "help" message for the user of the plugin.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.module.Module
Generates a "help" message for the user of the module.
get_syntax() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory
 
get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
Generates a "help" message for the user of the plugin.
get_syntax() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Generates a "help" message for the user of the plugin.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
Generates a "help" message for the user of the plugin.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
Generates a "help" message for the user of the plugin.
get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
get_workflow_info.
get_workflow_info(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
get_workflow_info.
get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
get_workflow_info.
get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
get_workflow_info.
get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
get_workflow_run_accession.
get_workflow_run_accession(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
get_workflow_run_accession.
get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
get_workflow_run_accession.
get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
get_workflow_run_accession.
get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
get_workflow_run_id.
get_workflow_run_id(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
get_workflow_run_id.
get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
get_workflow_run_id.
get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
get_workflow_run_id.
getABISOLID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
Gets the value of the abisolid property.
getAbstractStr() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field abstractStr.
getABUNDANCEMEASUREMENT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Gets the value of the abundancemeasurement property.
getAccess() - Method in class com.github.seqware.queryengine.model.interfaces.ACL
Get whether 0) owner can read, 1) owner can write, 2) group can read, 3) group can write, 4) other users can read 5) other users can write
getAccession() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field accession.
getAccession() - Method in class net.sourceforge.seqware.common.model.Organism
Getter for the field accession.
getAccession() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field accession.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the accession property.
getAccessionFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
getAccessionFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
getAcl() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
getAcl() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
getAcl() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
 
getAclBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
getAclOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
getAclOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
getAclOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
 
getACLs() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
getACLs.
getACTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS
Gets the value of the action property.
getACTIONS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the actions property.
getActive() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
Getter for the field active.
getActive() - Method in class net.sourceforge.seqware.common.model.ShareFile
Getter for the field active.
getActive() - Method in class net.sourceforge.seqware.common.model.ShareLane
Getter for the field active.
getActive() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
Getter for the field active.
getActive() - Method in class net.sourceforge.seqware.common.model.ShareSample
Getter for the field active.
getActive() - Method in class net.sourceforge.seqware.common.model.ShareStudy
Getter for the field active.
getActive() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
Getter for the field active.
getAdapters() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field adapters.
getAdapterSpec() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
Getter for the field adapterSpec.
getADAPTERSPEC() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
Gets the value of the adapterspec property.
getADD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Gets the value of the add property.
getAddedSurcharge() - Method in class net.sourceforge.seqware.common.model.Expense
Getter for the field addedSurcharge.
getAdditionalAttribute(String) - Method in class com.github.seqware.queryengine.model.Feature
Returns the value of an additional attribute or null of the attribute does not exist.
getAdditionalAttributeNames() - Method in class com.github.seqware.queryengine.model.Feature
Returns the names of the additional attributes stored.
getAdhoctagset() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Getter for the field adhoctagset.
getAgent() - Method in class net.sourceforge.seqware.common.model.Expense
Getter for the field agent.
getAlgo() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
get the job algorithm
getAlgorithm() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field algorithm.
getAlgorithm() - Method in class net.sourceforge.seqware.common.module.ReturnValue
Getter for the field algorithm.
getAlgorithm() - Method in class net.sourceforge.seqware.pipeline.module.Module
Getter for the field algorithm.
getAlgorithm() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
getAlgorithm.
getAlgorithm() - Method in class net.sourceforge.seqware.pipeline.module.TestModule
Getter for the field algorithm.
getAlias() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field alias.
getAlias() - Method in class net.sourceforge.seqware.common.model.IUS
Getter for the field alias.
getAlias() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field alias.
getAlias() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field alias.
getAlias() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the alias property.
getAlias() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the alias property.
getAlias() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the alias property.
getAlias() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Gets the value of the alias property.
getAlias() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Gets the value of the alias property.
getAlias() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the alias property.
getAlign() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
getAll() - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO
getAll.
getAll() - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
getAll.
getAll() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
getAll.
getAll() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
getAll.
getAll() - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
getAll.
getAll() - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
getAll.
getAllAtoms() - Method in class com.github.seqware.queryengine.backInterfaces.StorageInterface
For debugging or very non-optimal implementations
getAllAtoms() - Method in class com.github.seqware.queryengine.impl.HBaseStorage
For debugging or very non-optimal implementations
getAllAtoms() - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
For debugging or very non-optimal implementations
getAllAtoms() - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
For debugging or very non-optimal implementations
getAllAtomsForTable(String) - Method in class com.github.seqware.queryengine.impl.HBaseStorage
getAllAtomsForTable.
getAllFeatureListsForFeatureSet(FeatureSet) - Method in class com.github.seqware.queryengine.backInterfaces.StorageInterface
Iterate through all the feature "buckets" in a feature set, this might be moved later.
getAllFeatureListsForFeatureSet(FeatureSet) - Method in class com.github.seqware.queryengine.impl.HBaseStorage
Iterate through all the feature "buckets" in a feature set, this might be moved later.
getAllFeatureListsForFeatureSet(FeatureSet) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
Iterate through all the feature "buckets" in a feature set, this might be moved later.
getAllFeatureListsForFeatureSet(FeatureSet) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
Iterate through all the feature "buckets" in a feature set, this might be moved later.
getAllHtml(Lane, Registration, String, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
getAllHtml.
getAllHtml(IUS, Registration, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
getAllHtml.
getAllHtml(Processing, Registration, String, Integer, List<String>, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
getAllHtml.
getAllHtml(Processing, Registration, String, Integer, List<String>, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil
getAllHtml.
getAllHtml(IUS, Registration, String, Integer, List<String>, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil
getAllHtml.
getAllHtml(Study, Registration, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
getAllHtml.
getAllHtml(Experiment, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
getAllHtml.
getAllHtml(Sample, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
getAllHtml.
getAllHtml(Lane, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
getAllHtml.
getAllItems() - Method in class net.sourceforge.solexatools.util.PageInfo
Getter for the field allItems.
getAllProcessing() - Method in class net.sourceforge.seqware.common.model.SequencerRun
getAllProcessing.
getAllProcessings() - Method in class net.sourceforge.seqware.common.model.Lane
getAllProcessings.
getAllRuns() - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
Find all of the workflow runs, and report on each of the workflow runs the files, samples and processing events associated with each.
getAllSelectedFiles(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
Get all selected Files, the files are organized by the name of the parameter (key) and a list of files selected (value) via a hash.
getAllSequencerRuns() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getAllSequencerRuns() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
Get all of the sequencer runs in the DB.
getAllSequencerRuns() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getAllSequencerRuns() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getAllSequencerRuns.
getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
getAllStudies.
getAllStudies() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getAllStudies.
getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
getAllStudies.
getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getAllStudies.
getANALYSIS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisSet
Gets the value of the analysis property.
getANALYSISATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES
Gets the value of the analysisattribute property.
getANALYSISATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the analysisattributes property.
getAnalysisCenter() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the analysisCenter property.
getANALYSISFILES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the analysisfiles property.
getANALYSISLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS
Gets the value of the analysislink property.
getANALYSISLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the analysislinks property.
getAnalysisPlugins() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
getAnalysisPlugins.
getAnalysisSets() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
getAnalysisSets.
getANALYSISTYPE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the analysistype property.
getAnalysisWorkflowHtml(WorkflowRun, Registration, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
getAnalysisWorkflowHtml.
getAnonymizedName() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field anonymizedName.
getANONYMIZEDNAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
Gets the value of the anonymizedname property.
getApplication() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource
getApplicationInfo(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication
getApplicationInfo(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion
getArch() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
 
getArgs(String) - Method in class net.sourceforge.seqware.pipeline.runner.RunnerParams
getArgs.
getArgs(String, boolean) - Method in class net.sourceforge.seqware.pipeline.runner.RunnerParams
getArgs.
getArguments() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
 
getArguments() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
Getter for the field arguments.
getAsText() - Method in class net.sourceforge.solexatools.validation.CustomIntegerEditor
getAsText.
getAtom() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginPBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginRunPBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getAtom() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager.AtomStatePair
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getAtomBySGID(SGID) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
Find a object in the back-end by a globally unique SGID
getAtomBySGID(Class<T>, SGID) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
Find an object in the back-end when a specific class is known using a globally unique SGID while taking into account the timestamp
getAtomBySGID(SGID) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Deprecated. It is much more efficient to retrieve an Atom when you know the class
getAtomBySGID(Class<T>, SGID) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Find an object in the back-end when a specific class is known using a globally unique SGID while taking into account the timestamp
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginPBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginRunPBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getAtomsBySGID(Class<T>, SGID...) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
Find a batch of objects in the back-end when a specific class is known using a globally unique SGID while taking into account the timestamp
getAtomsBySGID(Class<T>, SGID...) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Find a batch of objects in the back-end when a specific class is known using a globally unique SGID while taking into account the timestamp
getAttribute(String) - Method in class com.github.seqware.queryengine.model.Feature
Generic implementation for retrieving the value of a GVF or additional attribute.
getAttribute(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
getAttribute.
getAttribute() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
Getter for the field attribute.
getAttribute() - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributeResource
getAttribute.
getAttribute() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource
getAttribute.
getAttributes() - Method in class net.sourceforge.seqware.common.module.ReturnValue
Getter for the field attributes.
getAttributes() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Getter for the field attributes.
getAttributes() - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto
Getter for the field attributes.
getBackendTimestamp() - Method in class com.github.seqware.queryengine.util.SGID
Getter for the field backendTimestamp.
getBarcode() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Get the value of barcode
getBarcode() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Getter for the field barcode.
getBarcodeSeqence() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
Gets the value of the barcodeSeqence property.
getBaseCaller() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field baseCaller.
getBASECALLER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS
Gets the value of the basecaller property.
getBASECALLS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING
Gets the value of the basecalls property.
getBaseCoord() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Getter for the field baseCoord.
getBASECOORD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Gets the value of the basecoord property.
getBaseDir() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Getter for the field baseDir.
getBaseIniFile() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field baseIniFile.
getBasePath() - Method in class com.github.seqware.queryengine.system.rest.QueryEngineServiceConfigReader
 
getBaseQualities() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field baseQualities.
getBatch_size() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Getter for the field batch_size.
getBinSize() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Getter for the field binSize.
getBinSize() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Getter for the field binSize.
getBlockCount() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Getter for the field blockCount.
getBlockSizes() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Getter for the field blockSizes.
getBlockStarts() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Getter for the field blockStarts.
getBrokerName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the brokerName property.
getBundle_version() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getBundleInfo(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
getBundleInfo.
getCacheSize() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Getter for the field cacheSize.
getCalledBase() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field calledBase.
getCalledBaseCount() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field calledBaseCount.
getCalledBaseCountForward() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field calledBaseCountForward.
getCalledBaseCountReverse() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field calledBaseCountReverse.
getCallOne() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field callOne.
getCallTwo() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field callTwo.
getCascade() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
getCascade() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
getCascade() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
 
getCascade() - Method in class com.github.seqware.queryengine.model.impl.AbstractMolSet
Return whether cascade should occur on deletion
getCascade() - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl
Return whether cascade should occur on deletion
getCascade() - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable
Return whether cascade should occur on deletion
getCell() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.Cells
 
getCenterName() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field centerName.
getCenterName() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field centerName.
getCenterName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the centerName property.
getCENTERNAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Gets the value of the centername property.
getCenterName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the centerName property.
getCenterProjectName() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field centerProjectName.
getCENTERPROJECTNAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Gets the value of the centerprojectname property.
getChecksum() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
Gets the value of the checksum property.
getChecksumMethod() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
Gets the value of the checksumMethod property.
getChildMaps() - Method in class com.github.seqware.queryengine.model.interfaces.Taggable.NestedLevel
 
getChildren() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field children.
getChildren() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field children.
getChildren() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
getChildren() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
getChildrenUrls() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Getter for the field childrenUrls.
getChildSample() - Method in class net.sourceforge.seqware.common.model.FileReportRow
Getter for the field childSample.
getChildSample() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
Getter for the field childSample.
getChildSample() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
Getter for the field childSample.
getChildSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
Getter for the field childSample.
getChildSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Getter for the field childSample.
getChildSamples(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
getChildSamples.
getChildSamples(Study) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
getChildSamples.
getChildSamples(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
getChildSamples.
getChildSamples(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
getChildSamples.
getChildSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getChildSamplesFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
Get the child samples of a parent sample.
getChildSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getChildSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getChildTags() - Method in class com.github.seqware.queryengine.model.interfaces.Taggable.NestedLevel
 
getClassesDir() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Getter for the field classesDir.
getClassName() - Method in class com.github.seqware.queryengine.system.rest.resources.FeatureSetResource
 
getClassName() - Method in class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
Names the class, useful for comments and debugging output
getClassName() - Method in class com.github.seqware.queryengine.system.rest.resources.GroupResource
 
getClassName() - Method in class com.github.seqware.queryengine.system.rest.resources.PluginResource
 
getClassName() - Method in class com.github.seqware.queryengine.system.rest.resources.PluginRunResource
 
getClassName() - Method in class com.github.seqware.queryengine.system.rest.resources.ReferenceResource
 
getClassName() - Method in class com.github.seqware.queryengine.system.rest.resources.ReferenceSetResource
 
getClassName() - Method in class com.github.seqware.queryengine.system.rest.resources.TagResource
 
getClassName() - Method in class com.github.seqware.queryengine.system.rest.resources.TagSetResource
 
getClassName() - Method in class com.github.seqware.queryengine.system.rest.resources.UserResource
 
getClassPath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
getClientNotes() - Method in class net.sourceforge.seqware.common.model.Invoice
Getter for the field clientNotes.
getCode() - Method in class net.sourceforge.seqware.common.model.Organism
Getter for the field code.
getCode() - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto
Getter for the field code.
getCodingStart() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field codingStart.
getCodingStop() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field codingStop.
getCOLOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX
Gets the value of the color property.
getColorMatrix() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field colorMatrix.
getColorMatrix() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field colorMatrix.
getCOLORMATRIX() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
Gets the value of the colormatrix property.
getColorMatrixCode() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field colorMatrixCode.
getColorMatrixCode() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field colorMatrixCode.
getCOLORMATRIXCODE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
Gets the value of the colormatrixcode property.
getCommand() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field command.
getCommand() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field command.
getCommand() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Getter for the field command.
getCommand() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
getCommand() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getCOMMONNAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
Gets the value of the commonname property.
getCompleted() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Getter for the field completed.
getCompute() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getComputeReq() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Getter for the field computeReq.
getConfigPath() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Getter for the field configPath.
getConfigs() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getConfiguration() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication
Getter for the field configuration.
getConfiguration() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion
Getter for the field configuration.
getConfirmEmailAddress() - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
Getter for the field confirmEmailAddress.
getConfirmPassword() - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
Getter for the field confirmPassword.
getConnectionString() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Getter for the field connectionString.
getConsensusAveSeqQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field consensusAveSeqQuality.
getConsensusBase() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field consensusBase.
getConsensusCallQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field consensusCallQuality.
getConsensusMaxSeqQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field consensusMaxSeqQuality.
getConsequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getConsequence.
getConsequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getConsequence.
getConsequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getConsequence.
getConsequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getConsequence.
getConsequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getConsequence.
getConsequence(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getConsequence.
getConsequencesByMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getConsequencesByMismatch.
getConsequencesByMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getConsequencesByMismatch.
getConsequencesByMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getConsequencesByMismatch.
getConsequencesByMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getConsequencesByMismatch.
getConsequencesByMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getConsequencesByMismatch.
getConsequencesByMismatch(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getConsequencesByMismatch.
getConsequencesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getConsequencesByTag.
getConsequencesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getConsequencesByTag.
getConsequencesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getConsequencesByTag.
getConsequencesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getConsequencesByTag.
getConsequencesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getConsequencesByTag.
getConsequencesByTag(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getConsequencesByTag.
getConsequenceTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getConsequenceTagsBySearch.
getConsequenceTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getConsequenceTagsBySearch.
getConsequenceTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getConsequenceTagsBySearch.
getConsequenceTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getConsequenceTagsBySearch.
getConsequenceTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getConsequenceTagsBySearch.
getConstructionProtocol() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Getter for the field constructionProtocol.
getCONTACT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS
Gets the value of the contact property.
getCONTACTS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the contacts property.
getContig() - Method in class net.sourceforge.seqware.queryengine.backend.model.ContigPosition
Getter for the field contig.
getContig() - Method in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
Getter for the field contig.
getContig() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field contig.
getContig() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
Getter for the field contig.
getCount() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl.TagValueIterable
 
getCount() - Method in class com.github.seqware.queryengine.model.impl.hbasemrlazy.MRLazyFeatureSet
Get number of elements in set
getCount() - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
Get number of elements in set
getCount() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
Get number of elements in set
getCount() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
Get number of elements in set
getCount() - Method in class com.github.seqware.queryengine.util.InMemoryIterable
Get number of elements in set
getCount() - Method in interface com.github.seqware.queryengine.util.SeqWareIterable
Get number of elements in set
getCount() - Method in class com.github.seqware.queryengine.util.SGIDIterable
Get number of elements in set
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage
Getter for the field count.
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator
getCount.
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator
Not supported for HBase backend!
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator
Not supported for HBase backend!
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator
Not supported for this backend!
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator
Not supported for this backend!
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator
Not supported for this backend!
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator
getCount.
getCount() - Method in interface net.sourceforge.seqware.queryengine.backend.util.SeqWareIterator
getCount.
getCountFile() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field countFile.
getCountFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
getCountFiles.
getCountFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
getCountFiles.
getCountFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
getCountFiles.
getCountFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
getCountFiles.
getCoverage(Integer) - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage
Getter for the field coverage.
getCoverage() - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage
Getter for the field coverage.
getCoverages(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getCoverages.
getCoverages(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getCoverages.
getCoverages(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getCoverages.
getCoverages(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getCoverages.
getCoverages(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getCoverages.
getCoverages(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getCoverages.
getCoverages(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getCoverages.
getCoverages(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getCoverages.
getCoverages(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getCoverages.
getCoverages(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getCoverages.
getCoverages(String, int, int) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getCoverages.
getCoverages(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getCoverages.
getCreated() - Method in class net.sourceforge.seqware.common.model.SampleSearch
Getter for the field created.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Invoice
Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.IUS
Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Project
Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Registration
Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareStudy
Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field createTimestamp.
getCreateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Getter for the field createTimeStamp.
getCreateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Getter for the field createTimeStamp.
getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
Getter for the field createTstmp.
getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareFile
Getter for the field createTstmp.
getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareLane
Getter for the field createTstmp.
getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
Getter for the field createTstmp.
getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareSample
Getter for the field createTstmp.
getCriteria() - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
Getter for the field criteria.
getCurrentSelectedFiles(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
getCurrentSelectedFiles.
getCurrentSelectedNodes(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
getCurrentSelectedNodes.
getCurrentWorkflow(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
getCurrentWorkflow.
getCurrentWorkflowParam(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
getCurrentWorkflowParam.
getCurrentWorkingDir() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field currentWorkingDir.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator
Getter for the field cursor.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator
Not applicable for HBase backend.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator
Not applicable for HBase backend.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator
Not applicable for Postgres backend.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator
Not applicable for Postgres backend.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator
Not applicable for Postgres backend.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator
Getter for the field cursor.
getCursor() - Method in interface net.sourceforge.seqware.queryengine.backend.util.SeqWareIterator
getCursor.
getCwd() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field cwd.
getCycleCoord() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Getter for the field cycleCoord.
getCYCLECOORD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Gets the value of the cyclecoord property.
getCycleCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field cycleCount.
getCycleCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field cycleCount.
getCYCLECOUNT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
Gets the value of the cyclecount property.
getCYCLECOUNT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
Gets the value of the cyclecount property.
getCycleDescriptor() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field cycleDescriptor.
getCycleDescriptor() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field cycleDescriptor.
getCycleDescriptor() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field cycleDescriptor.
getCycles() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field cycles.
getCycles() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field cycles.
getCycleSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field cycleSequence.
getCycleSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field cycleSequence.
getCYCLESEQUENCE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
Gets the value of the cyclesequence property.
getData() - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
Getter for the field data.
getDatabase() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Getter for the field database.
getDATABLOCK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the datablock property.
getDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getDate() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getDate() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getDate() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getDate() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getDax() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field dax.
getDaxDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getDaysUntilDue() - Method in class net.sourceforge.seqware.common.model.Invoice
Getter for the field daysUntilDue.
getDb() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
Getter for the field db.
getDb() - Method in class net.sourceforge.seqware.common.model.ExperimentLink
Getter for the field db.
getDb() - Method in class net.sourceforge.seqware.common.model.IUSLink
Getter for the field db.
getDb() - Method in class net.sourceforge.seqware.common.model.LaneLink
Getter for the field db.
getDb() - Method in class net.sourceforge.seqware.common.model.SampleLink
Getter for the field db.
getDb() - Method in class net.sourceforge.seqware.common.model.StudyLink
Getter for the field db.
getDB() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
Gets the value of the db property.
getDB() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
Gets the value of the db property.
getDB() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
Gets the value of the db property.
getDB() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK
Gets the value of the db property.
getDB() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
Gets the value of the db property.
getDB() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
Gets the value of the db property.
getDbmd() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
Getter for the field dbmd.
getDecodeMethod() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
Getter for the field decodeMethod.
getDecryptCipher(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Gets cipher by DecryptKey.
getDecryptCipher() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
getDecryptCipher.
getDefaultDirManagerExcutable(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.WorkflowExecutableUtils
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getDefaultJavaExcutable(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.WorkflowExecutableUtils
 
getDefaultJavaLocalExcutable(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.WorkflowExecutableUtils
 
getDefaultPerlExcutable(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.WorkflowExecutableUtils
 
getDefaultValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Getter for the field defaultValue.
getDelegates() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
getDelegates.
getDelegates() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
getDelegates.
getDENOVOASSEMBLY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Gets the value of the denovoassembly property.
getDependentElement(PegasusJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
getDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getDescription() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getDescription() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
getDescription() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginPBOrBuilder
 
getDescription() - Method in class com.github.seqware.queryengine.model.FeatureSet
Get the description associated with this FeatureSet
getDescription() - Method in interface com.github.seqware.queryengine.model.Group
Get the description associated with this group
getDescription() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
Get the description associated with this FeatureSet
getDescription() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
Get the description associated with this group
getDescription() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryPlugin
Get the description associated with this plugin
getDescription() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
Get the description associated with this FeatureSet
getDescription() - Method in interface com.github.seqware.queryengine.model.Plugin
Get the description associated with this plugin
getDescription() - Method in class net.sourceforge.seqware.common.model.Expense
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.File
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.IUS
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.LibrarySource
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.Platform
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.Project
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.StudyType
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
getDescription() - Method in class net.sourceforge.seqware.common.module.ReturnValue
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Getter for the field description.
getDESCRIPTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the description property.
getDESCRIPTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Gets the value of the description property.
getDescription() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Getter for the field description.
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getDescriptor() - Static method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Gets the value of the descriptor property.
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getDescriptorForType() - Method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getDESIGN() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the design property.
getDESIGNDESCRIPTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
Gets the value of the designdescription property.
getDestSet() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner.PluginRunnerMapper
 
getDestSet() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryPluginRunner
 
getDestSet() - Method in interface com.github.seqware.queryengine.plugins.MapperInterface
 
getDibase() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
Gets the value of the dibase property.
getDirContext() - Method in class net.sourceforge.solexatools.authentication.OICRLdapAuthentication
getDirContext.
getDirectories() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getDirectoriesNumber() - Method in class net.sourceforge.solexatools.util.FileFinder
Getter for the field directoriesNumber.
getDirectorySize() - Method in class net.sourceforge.solexatools.util.FileFinder
getDirectorySize.
getDisplay() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Getter for the field display.
getDisplay() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
getDisplayName() - Method in class net.sourceforge.seqware.common.model.FileType
Getter for the field displayName.
getDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Getter for the field displayName.
getDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
Getter for the field displayName.
getDisplayName() - Method in class net.sourceforge.solexatools.util.SummaryLine
Getter for the field displayName.
getDisplayValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Getter for the field displayValue.
getDomainObject() - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
Getter for the field domainObject.
getDomainObject() - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
Getter for the field domainObject.
getElements() - Method in class com.github.seqware.queryengine.system.rest.resources.FeatureSetResource
 
getElements() - Method in class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
Iterate through the elements of this type
getElements() - Method in class com.github.seqware.queryengine.system.rest.resources.GroupResource
 
getElements() - Method in class com.github.seqware.queryengine.system.rest.resources.PluginResource
 
getElements() - Method in class com.github.seqware.queryengine.system.rest.resources.PluginRunResource
 
getElements() - Method in class com.github.seqware.queryengine.system.rest.resources.ReferenceResource
 
getElements() - Method in class com.github.seqware.queryengine.system.rest.resources.ReferenceSetResource
 
getElements() - Method in class com.github.seqware.queryengine.system.rest.resources.TagResource
 
getElements() - Method in class com.github.seqware.queryengine.system.rest.resources.TagSetResource
 
getElements() - Method in class com.github.seqware.queryengine.system.rest.resources.UserResource
 
getEmail() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
Getter for the field email.
getEmailAddress() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getEmailAddress() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getEmailAddress() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getEmailAddress() - Method in class com.github.seqware.queryengine.model.User
Get email address
getEmailAddress() - Method in class net.sourceforge.seqware.common.model.Registration
Getter for the field emailAddress.
getEncryptCipher(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Gets cipher by EncryptKey.
getEncryptCipher() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
getEncryptCipher.
getEnd() - Method in class net.sourceforge.seqware.common.model.UploadSequence
Getter for the field end.
getEndDate() - Method in class net.sourceforge.seqware.common.model.Invoice
Getter for the field endDate.
getEndPage() - Method in class net.sourceforge.solexatools.util.PageInfo
Getter for the field endPage.
getEntityUrl() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
Getter for the field entityUrl.
getENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
Gets the value of the entrezlink property.
getENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
Gets the value of the entrezlink property.
getENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK
Gets the value of the entrezlink property.
getENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK
Gets the value of the entrezlink property.
getENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK
Gets the value of the entrezlink property.
getEnv() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getError() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
Getter for the field error.
getErrorCnt(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
getErrorCnt.
getErrorCnt(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
getErrorCnt.
getErrorCnt() - Method in class net.sourceforge.seqware.common.model.Lane
getErrorCnt.
getErrorCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRun
getErrorCnt.
getErrorCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
getErrorCnt.
getErrorCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field errorCount.
getExecutionEnv() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getExistingStudyType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE
Gets the value of the existingStudyType property.
getExistingType() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field existingType.
getExistingTypeInt() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field existingTypeInt.
getExitCode() - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException
getExitCode.
getExitCode() - Method in exception net.sourceforge.seqware.common.err.SeqwareException
getExitCode.
getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwBadFileException
getExitCode.
getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwBadModuleException
getExitCode.
getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwParameterException
getExitCode.
getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwRunnerParameterException
getExitCode.
getExitStatus() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field exitStatus.
getExitStatus() - Method in class net.sourceforge.seqware.common.module.ReturnValue
Getter for the field exitStatus.
getExpectedBaseCall() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Getter for the field expectedBaseCall.
getEXPECTEDBASECALL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Gets the value of the expectedbasecall property.
getExpectedNumberReads() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field expectedNumberReads.
getExpectedNumberReads() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the expectedNumberReads property.
getExpectedNumberRuns() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field expectedNumberRuns.
getExpectedNumberRuns() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the expectedNumberRuns property.
getExpectedNumberSpots() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field expectedNumberSpots.
getExpectedNumberSpots() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the expectedNumberSpots property.
getExpectedNumReads() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field expectedNumReads.
getExpectedNumRuns() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field expectedNumRuns.
getExpectedNumSpots() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field expectedNumSpots.
getExpenseId() - Method in class net.sourceforge.seqware.common.model.Expense
Getter for the field expenseId.
getExpenses() - Method in class net.sourceforge.seqware.common.model.Invoice
Getter for the field expenses.
getExpenseType() - Method in class net.sourceforge.seqware.common.model.Expense
Getter for the field expenseType.
getExperiment() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
Getter for the field experiment.
getExperiment() - Method in class net.sourceforge.seqware.common.model.ExperimentLink
Getter for the field experiment.
getExperiment() - Method in class net.sourceforge.seqware.common.model.FileReportRow
Getter for the field experiment.
getExperiment() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
Getter for the field experiment.
getExperiment() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field experiment.
getExperiment() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
Getter for the field experiment.
getEXPERIMENT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentSet
Gets the value of the experiment property.
getEXPERIMENTATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES
Gets the value of the experimentattribute property.
getExperimentAttributeId() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
Getter for the field experimentAttributeId.
getExperimentAttributes() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field experimentAttributes.
getEXPERIMENTATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the experimentattributes property.
getExperimentHtml(Experiment, Registration, String, String, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
getExperimentHtml.
getExperimentId() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field experimentId.
getExperimentLibraryDesign() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field experimentLibraryDesign.
getExperimentLibraryDesignId() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Getter for the field experimentLibraryDesignId.
getExperimentLibraryDesignService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Getter for the field experimentLibraryDesignService.
getEXPERIMENTLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS
Gets the value of the experimentlink property.
getExperimentLinkId() - Method in class net.sourceforge.seqware.common.model.ExperimentLink
Getter for the field experimentLinkId.
getExperimentLinks() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field experimentLinks.
getEXPERIMENTLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the experimentlinks property.
getEXPERIMENTREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Gets the value of the experimentref property.
getEXPERIMENTREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the experimentref property.
getExperiments() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field experiments.
getExperiments() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field experiments.
getExperimentService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
Getter for the field experimentService.
getExperimentServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getExperimentServiceBean.
getExperimentsFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getExperimentsFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
Get experiments from a study.
getExperimentsFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getExperimentsFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getExperimentSpotDesign() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field experimentSpotDesign.
getExperimentSpotDesign() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Getter for the field experimentSpotDesign.
getExperimentSpotDesignId() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
Getter for the field experimentSpotDesignId.
getExperimentSpotDesignReadSpecId() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Getter for the field experimentSpotDesignReadSpecId.
getExperimentSpotDesignReadSpecService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Getter for the field experimentSpotDesignReadSpecService.
getExperimentSpotDesignService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Getter for the field experimentSpotDesignService.
getExperimentSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getExpiryDate() - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl
Return the expiry date
getExpiryDate() - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable
Return the expiry date
getExpiryTime() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
getExpiryTime() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
getExpiryTime() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
 
getExpiryTime() - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl
Return raw expiry time
getExpiryTime() - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable
Return raw expiry time
getExpLibDesignDesc() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field expLibDesignDesc.
getExpLibDesignName() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field expLibDesignName.
getExpLibDesignProtocol() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field expLibDesignProtocol.
getExpLibDesignSelection() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field expLibDesignSelection.
getExpLibDesignSource() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field expLibDesignSource.
getExpLibDesignStrategy() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field expLibDesignStrategy.
getExpSpotDesignAdapterSpec() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field expSpotDesignAdapterSpec.
getExpSpotDesignReadsPerSpot() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field expSpotDesignReadsPerSpot.
getExpSpotDesignTagSpec() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field expSpotDesignTagSpec.
getExt_parameters() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner.PluginRunnerMapper
 
getExt_parameters() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryPluginRunner
 
getExt_parameters() - Method in interface com.github.seqware.queryengine.plugins.MapperInterface
 
getExtension() - Method in class net.sourceforge.seqware.common.model.FileType
Getter for the field extension.
getExtension(String) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
getExtension.
getExternalId() - Method in class net.sourceforge.seqware.common.model.Invoice
Getter for the field externalId.
getExternalSerializationVersion() - Method in interface com.github.seqware.queryengine.model.Atom
Get the serializationVersion for this particular atom.
getExternalSerializationVersion() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Get the serializationVersion for this particular atom.
getFailed() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Getter for the field failed.
getFailedCount(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
getFailedCount.
getFailedCount(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
getFailedCount.
getFailedJobsInfo(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
This method will examine a Pegasus DAX log directory for a given workflow and identify the log files for jobs that failed.
getFastqConvNum() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Getter for the field fastqConvNum.
getFastqConvNum() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Getter for the field fastqConvNum.
getFeature() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Getter for the field feature.
getFeature(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
getFeature.
getFeature(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getFeature.
getFeature(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getFeature.
getFeature(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getFeature.
getFeature(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getFeature.
getFeature(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getFeature.
getFeature(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getFeature.
getFeatures(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getFeatures(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getFeatures(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
 
getFeatures(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getFeatures(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getFeatures(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getFeatures(int, FeatureSet) - Method in class com.github.seqware.queryengine.impl.MRHBasePersistentBackEnd
(Do not) filter features
getFeatures(int, FeatureSet) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
(Do not) filter features
getFeatures() - Method in class com.github.seqware.queryengine.model.FeatureSet
Get the list of features associated with this feature set.
getFeatures() - Method in class com.github.seqware.queryengine.model.impl.FeatureList
Returns a list of features at this location, should not be modified.
getFeatures() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
Get the list of features associated with this feature set.
getFeatures() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
Get the list of features associated with this feature set.
getFeatures(int, FeatureSet) - Method in interface com.github.seqware.queryengine.model.QueryInterface
(Do not) filter features
getFeatures(String, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
getFeatures.
getFeatures() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getFeatures.
getFeatures(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getFeatures.
getFeatures() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getFeatures.
getFeatures(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getFeatures.
getFeatures() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getFeatures.
getFeatures(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getFeatures.
getFeatures() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getFeatures.
getFeatures(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getFeatures.
getFeatures() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getFeatures.
getFeatures(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getFeatures.
getFeatures() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getFeatures.
getFeatures(String, int, int) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getFeatures.
getFeaturesBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getFeaturesBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getFeaturesBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getFeaturesBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getFeaturesByAttributes(int, FeatureSet, RPNStack) - Method in class com.github.seqware.queryengine.impl.MRHBasePersistentBackEnd
Filter features by a range of attributes.
getFeaturesByAttributes(int, FeatureSet, RPNStack) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
Filter features by a range of attributes.
getFeaturesByAttributes(int, FeatureSet, RPNStack) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Filter features by a range of attributes.
getFeaturesByPlugin(int, Class<? extends PluginInterface>, FeatureSet, Object...) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
Call an arbitrary installed plug-in by class and initiate it
getFeaturesByPlugin(int, Class<? extends PluginInterface>, FeatureSet, Object...) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Call an arbitrary installed plug-in by class and initiate it
getFeaturesByRange(int, FeatureSet, QueryInterface.Location, String, long, long) - Method in class com.github.seqware.queryengine.impl.MRHBasePersistentBackEnd
filter features that overlap with a given range
getFeaturesByRange(int, FeatureSet, QueryInterface.Location, String, long, long) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
filter features that overlap with a given range
getFeaturesByRange(int, FeatureSet, QueryInterface.Location, String, long, long) - Method in interface com.github.seqware.queryengine.model.QueryInterface
filter features that overlap with a given range
getFeaturesByTag(int, FeatureSet, String, String, String) - Method in class com.github.seqware.queryengine.impl.MRHBasePersistentBackEnd
filter features with tags.
getFeaturesByTag(int, FeatureSet, String, String, String) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
filter features with tags.
getFeaturesByTag(int, FeatureSet, String, String, String) - Method in interface com.github.seqware.queryengine.model.QueryInterface
filter features with tags.
getFeaturesByTag(String, Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer, String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
getFeaturesByTag.
getFeaturesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getFeaturesByTag.
getFeaturesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getFeaturesByTag.
getFeaturesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getFeaturesByTag.
getFeaturesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getFeaturesByTag.
getFeaturesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getFeaturesByTag.
getFeaturesByTag(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getFeaturesByTag.
getFeaturesCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getFeaturesCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getFeaturesCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
 
getFeaturesCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getFeaturesCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getFeaturesCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getFeatureSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getFeatureSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getFeatureSet() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
getFeatureSetBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getFeatureSetCount(int, FeatureSet) - Method in class com.github.seqware.queryengine.impl.MRHBasePersistentBackEnd
Get the number of features in a feature set
getFeatureSetCount(int, FeatureSet) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
Get the number of features in a feature set
getFeatureSetCount(int, FeatureSet) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Get the number of features in a feature set
getFeatureSetID() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Getter for the field featureSetID.
getFeatureSetID() - Method in class com.github.seqware.queryengine.util.FSGID
Get the ID for the associated feature set
getFeatureSetIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getFeatureSetIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getFeatureSetIDs(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getFeatureSetIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getFeatureSetIDsBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getFeatureSetIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getFeatureSetIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getFeatureSetIDsCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getFeatureSetIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getFeatureSetIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getFeatureSetIDsList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getFeatureSetIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getFeatureSetIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getFeatureSetIDsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getFeatureSetIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getFeatureSetIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getFeatureSetIDsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getFeatureSetOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getFeatureSetOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getFeatureSetOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
getFeatureSets() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd
getFeatureSets.
getFeatureSets() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
getFeatureSets.
getFeatureSets() - Method in interface com.github.seqware.queryengine.model.QueryInterface
getFeatureSets.
getFeatureSets() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
getFeatureSets.
getFeaturesList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getFeaturesList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getFeaturesList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
 
getFeaturesList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getFeaturesList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getFeaturesList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getFeaturesOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getFeaturesOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getFeaturesOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
 
getFeaturesOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getFeaturesOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getFeaturesOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getFeaturesOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
getFeaturesOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getFeaturesOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
 
getFeaturesOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getFeaturesOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getFeaturesOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getFeaturesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getFeaturesTags.
getFeaturesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getFeaturesTags.
getFeaturesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getFeaturesTags.
getFeaturesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getFeaturesTags.
getFeaturesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getFeaturesTags.
getFeaturesTags() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getFeaturesTags.
getFeaturesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getFeaturesUnordered.
getFeaturesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getFeaturesUnordered.
getFeaturesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getFeaturesUnordered.
getFeaturesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getFeaturesUnordered.
getFeaturesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getFeaturesUnordered.
getFeaturesUnordered() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getFeaturesUnordered.
getFeatureTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getFeatureTagsBySearch.
getFeatureTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getFeatureTagsBySearch.
getFeatureTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getFeatureTagsBySearch.
getFeatureTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getFeatureTagsBySearch.
getFeatureTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getFeatureTagsBySearch.
getFile() - Method in class net.sourceforge.seqware.common.business.UploadFile
Getter for the field file.
getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
getFile.
getFile(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getFile.
getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
getFile.
getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getFile.
getFile() - Method in class net.sourceforge.seqware.common.model.FileAttribute
Getter for the field file.
getFile() - Method in class net.sourceforge.seqware.common.model.FileReportRow
Getter for the field file.
getFile() - Method in class net.sourceforge.seqware.common.model.ShareFile
Getter for the field file.
getFILE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES
Gets the value of the file property.
getFILE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES
Gets the value of the file property.
getFILE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES
Gets the value of the file property.
getFile() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
Getter for the field file.
getFileAttributeId() - Method in class net.sourceforge.seqware.common.model.FileAttribute
Getter for the field fileAttributeId.
getFileAttributes(Integer) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService
Returns a complete set of attributes for a give File.
getFileAttributes(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl
Returns a complete set of attributes for a give File.
getFileAttributes() - Method in class net.sourceforge.seqware.common.model.File
Getter for the field fileAttributes.
getFileAttributes() - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributesResource
getFileAttributes.
getFileAttributes() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributesServerResource
getFileAttributes.
getFileAttributeService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field fileAttributeService.
getFileAttributeServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getFileAttributeServiceBean.
getFileHtml(Processing, Registration) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
getFileHtml.
getFileHtml(Processing, Registration, List<String>, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil
getFileHtml.
getFileHtml(Processing, WorkflowRun, Registration, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
getFileHtml.
getFileId() - Method in class net.sourceforge.seqware.common.model.File
Getter for the field fileId.
getFileMetaType() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Getter for the field fileMetaType.
getFileMetaType() - Method in class net.sourceforge.solexatools.util.SummaryLine
Getter for the field fileMetaType.
getFilename() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getFileName() - Method in class net.sourceforge.seqware.common.model.File
getFileName.
getFilename(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
getFileName() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Gets the file name.
getFilename() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
getFilename() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE
Gets the value of the filename property.
getFilename() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE
Gets the value of the filename property.
getFilename() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
Gets the value of the filename property.
getFileName(String) - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController
getFileName.
getFileOne() - Method in class net.sourceforge.seqware.common.model.UploadSequence
Getter for the field fileOne.
getFilePath() - Method in class net.sourceforge.seqware.common.model.File
Getter for the field filePath.
getFilePath() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field filePath.
getFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field filePath.
getFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field filePath.
getFilePath() - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
getFilePath(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
 
getFilePath() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Getter for the field filePath.
getFilePath(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
getFilePath.
getFilePath() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
Getter for the field filePath.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.FileService
getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.FileService
getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService
getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.IUSService
getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService
getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.LaneService
getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService
getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.SampleService
getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService
getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.StudyService
getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
getFiles.
getFiles() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field files.
getFiles() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Getter for the field files.
getFiles() - Method in class net.sourceforge.seqware.common.module.ReturnValue
Getter for the field files.
getFiles() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getFiles() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
getFILES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Gets the value of the files property.
getFILES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the files property.
getFiles(HttpServletRequest, String) - Static method in class net.sourceforge.solexatools.util.BulkUtil
getFiles.
getFiles() - Method in class net.sourceforge.solexatools.util.SummaryLine
Getter for the field files.
getFiles_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Getter for the field files_url.
getFilesArray() - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
Getter for the field filesArray.
getFileService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController
Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloaderController
Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.FileController
Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.FileSetupController
Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController
Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
Getter for the field fileService.
getFileServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getFileServiceBean.
getFileSize(String) - Static method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
getFileSize.
getFilesNumber() - Method in class net.sourceforge.solexatools.util.FileFinder
Getter for the field filesNumber.
getFileStatus() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
getFileSwa() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getFileTwo() - Method in class net.sourceforge.seqware.common.model.UploadSequence
Getter for the field fileTwo.
getFileTwoURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
Getter for the field fileTwoURL.
getFileType() - Method in class net.sourceforge.seqware.common.business.UploadFile
Getter for the field fileType.
getFileType() - Method in class net.sourceforge.seqware.common.model.File
Getter for the field fileType.
getFileType() - Method in class net.sourceforge.seqware.common.model.UploadSequence
Getter for the field fileType.
getFiletype() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE
Gets the value of the filetype property.
getFiletype() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE
Gets the value of the filetype property.
getFileTypeId() - Method in class net.sourceforge.seqware.common.business.UploadFile
Getter for the field fileTypeId.
getFileTypeId() - Method in class net.sourceforge.seqware.common.model.FileType
Getter for the field fileTypeId.
getFileTypeId() - Method in class net.sourceforge.seqware.common.model.UploadSequence
Getter for the field fileTypeId.
getFileTypeService() - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
Getter for the field fileTypeService.
getFileTypeService() - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
Getter for the field fileTypeService.
getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Getter for the field fileTypeService.
getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
Getter for the field fileTypeService.
getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
Getter for the field fileTypeService.
getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
Getter for the field fileTypeService.
getFileUploadService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Getter for the field fileUploadService.
getFileURL() - Method in class net.sourceforge.seqware.common.business.UploadFile
Getter for the field fileURL.
getFileURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
Getter for the field fileURL.
getFileValidationServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getFileValidationServiceBean.
getFilter() - Method in class com.github.seqware.queryengine.plugins.plugins.FeaturesAllPlugin
getFilter.
getFilter() - Method in class com.github.seqware.queryengine.plugins.plugins.FeaturesByAttributesPlugin
getFilter.
getFilter() - Method in class com.github.seqware.queryengine.plugins.plugins.FeaturesByFilterPlugin
getFilter.
getFilter() - Method in class com.github.seqware.queryengine.plugins.plugins.FeaturesByRangePlugin
getFilter.
getFilter() - Method in class com.github.seqware.queryengine.plugins.plugins.FeaturesByTagPlugin
getFilter.
getFinishedCount(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
getFinishedCount.
getFinishedCount(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
getFinishedCount.
getFinishedTimestamp() - Method in class net.sourceforge.seqware.common.model.Expense
Getter for the field finishedTimestamp.
getFirstId(String) - Static method in class net.sourceforge.solexatools.util.Constant
getFirstId.
getFirstName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getFirstName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getFirstName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getFirstName() - Method in class com.github.seqware.queryengine.model.User
Get first name
getFirstName() - Method in class net.sourceforge.seqware.common.model.Registration
Getter for the field firstName.
getFirstName() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
Getter for the field firstName.
getFlowCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field flowCount.
getFlowCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field flowCount.
getFLOWCOUNT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
Gets the value of the flowcount property.
getFLOWCOUNT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
Gets the value of the flowcount property.
getFlowSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field flowSequence.
getFlowSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field flowSequence.
getFLOWSEQUENCE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
Gets the value of the flowsequence property.
getFLOWSEQUENCE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
Gets the value of the flowsequence property.
getFolderStore() - Method in class net.sourceforge.seqware.common.business.UploadFile
Getter for the field folderStore.
getFolderStore() - Method in class net.sourceforge.seqware.common.model.UploadSequence
Getter for the field folderStore.
getForceRunAll() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
getFormatCode() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Gets the value of the formatCode property.
getFrame() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Getter for the field frame.
getFriendlyRowkey() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
getFriendlyRowkey() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
getFriendlyRowkey() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
 
getFriendlyRowKey() - Method in class com.github.seqware.queryengine.util.SGID
Getter for the field friendlyRowKey.
getFs_default_name() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getFs_defaultFS() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getFs_hdfs_impl() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getFullName() - Method in class net.sourceforge.seqware.common.model.Workflow
getFullName.
getFuzzyStartPositionMax() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field fuzzyStartPositionMax.
getFuzzyStopPositionMin() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field fuzzyStopPositionMin.
getGcrOutputFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
 
getGeneChr() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field geneChr.
getGeneId() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field geneId.
getGeneId() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Getter for the field geneId.
getGenomeId() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Getter for the field genomeId.
getGenomicSequence() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field genomicSequence.
getGrammarFileName() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
getGrammarFileName.
getGrammarFileName() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
getGrammarFileName.
getGroup() - Method in class com.github.seqware.queryengine.model.interfaces.ACL
Get the group for the object
getGroup() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Getter for the field group.
getGroupingStrategy() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
getGroups() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd
Get all groups
getGroups() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
Get all groups
getGroups() - Method in interface com.github.seqware.queryengine.model.QueryInterface
Get all groups
getGroups() - Method in class com.github.seqware.queryengine.model.User
Get list of groups that this user is a part of
getGroups() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
getGroups.
getGroupSGID() - Method in class com.github.seqware.queryengine.model.interfaces.ACL
Get the group for the object
getGrp() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getGrp() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getGrp() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
 
getGrpBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getGrpOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getGrpOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getGrpOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
 
getGrps(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getGrps(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getGrps(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getGrpsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getGrpsBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getGrpsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getGrpsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getGrpsCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getGrpsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getGrpsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getGrpsList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getGrpsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getGrpsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getGrpsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getGrpsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getGrpsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getGrpsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getHandle() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the handle property.
getHbase_master() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getHbase_zookeeper_property_clientPort() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getHbase_zookeeper_quorum() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getHBaseClass() - Method in class com.github.seqware.queryengine.model.Feature
Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.FeatureList
Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryPlugin
Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference
Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet
Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.PluginRun
 
getHBaseClass() - Method in class com.github.seqware.queryengine.model.Tag
Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.User
Get the model class for the HBase where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.Feature
Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.FeatureList
Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryPlugin
Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference
Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet
Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.PluginRun
 
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.Tag
Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.User
Get the HBase table prefix where this obj should be stored
getHeader() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
Deprecated. 
getHeader() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.RunInfo
 
getHeader() - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource
getHeader.
getHELICOS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
Gets the value of the helicos property.
getHOLD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Gets the value of the hold property.
getHoldForPeriod() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
Gets the value of the holdForPeriod property.
getHoldUntilDate() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
Gets the value of the holdUntilDate property.
getHost() - Method in class net.sourceforge.seqware.common.model.Workflow
Deprecated.  
getHost() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field host.
getHost() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Getter for the field host.
getHtml() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field html.
getHtml() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field html.
getHtml() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field html.
getHtml(Object, Registration, List<String>, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
getHtml.
getHtml(Object, Registration, List<String>, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil
getHtml.
getHtml(Object, Registration, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
getHtml.
getHtml(WorkflowRun, Registration, String, boolean, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
getHtml.
getHtml(Sample, WorkflowRun, Registration, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
getHtml.
getHtml(Processing, WorkflowRun, Registration, String, List<String>, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
getHtml.
getHttpInputStream(String, int, long) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
getHttpInputStream.
getHYBRIDASSEMBLY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Gets the value of the hybridassembly property.
getId() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getId() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getId() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getId() - Method in class net.sourceforge.seqware.common.business.UploadFile
Getter for the field id.
getId() - Method in class net.sourceforge.seqware.common.model.ExperimentLink
Getter for the field id.
getId() - Method in class net.sourceforge.seqware.common.model.IUSLink
Getter for the field id.
getId() - Method in class net.sourceforge.seqware.common.model.LaneLink
Getter for the field id.
getId() - Method in class net.sourceforge.seqware.common.model.SampleLink
Getter for the field id.
getId() - Method in class net.sourceforge.seqware.common.model.StudyLink
Getter for the field id.
getId() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowEngine
 
getId() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine
 
getId() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
get the job id
getId() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.PegasusWorkflowEngine
 
getId() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field id.
getId() - Method in class net.sourceforge.seqware.queryengine.backend.model.Model
Getter for the field id.
getId() - Method in interface net.sourceforge.seqware.queryengine.backend.model.ModelInterface
getId.
getId() - Method in class net.sourceforge.seqware.queryengine.backend.model.StringId
Getter for the field id.
getID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
Gets the value of the id property.
getID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
Gets the value of the id property.
getID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
Gets the value of the id property.
getID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK
Gets the value of the id property.
getID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
Gets the value of the id property.
getID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
Gets the value of the id property.
getId() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
Getter for the field id.
getId(String) - Static method in class net.sourceforge.solexatools.util.Constant
getId.
getIdentitySamples() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
Getter for the field identitySamples.
getIdsSelectedLane(HttpServletRequest, WorkflowParam) - Method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
getIdsSelectedLane.
getILLUMINA() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
Gets the value of the illumina property.
getIndividualName() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field individualName.
getInfo() - Method in class net.sourceforge.seqware.common.model.FileType
getInfo.
getInfo() - Method in class net.sourceforge.solexatools.util.PageInfo
Getter for the field info.
getInformOnError() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
Gets the value of the informOnError property.
getInformOnStatus() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
Gets the value of the informOnStatus property.
getIniFile() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field iniFile.
getInput() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Getter for the field input.
getInput() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Getter for the field input.
getInputAlgorithm() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field inputAlgorithm.
getInputFiles() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
Getter for the field inputFiles.
getInstance() - Static method in class net.sourceforge.seqware.common.ContextImpl
getInstance.
getInstance() - Static method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter
 
getInstitution() - Method in class net.sourceforge.seqware.common.model.Registration
Getter for the field institution.
getInstitution() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
Getter for the field institution.
getInstrumentModel() - Method in class net.sourceforge.seqware.common.model.Platform
Getter for the field instrumentModel.
getINSTRUMENTMODEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
Gets the value of the instrumentmodel property.
getINSTRUMENTMODEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
Gets the value of the instrumentmodel property.
getINSTRUMENTMODEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
Gets the value of the instrumentmodel property.
getINSTRUMENTMODEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
Gets the value of the instrumentmodel property.
getInstrumentModel() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the instrumentModel property.
getInstrumentName() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field instrumentName.
getInstrumentName() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field instrumentName.
getInstrumentName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the instrumentName property.
getInt_parameters() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner.PluginRunnerMapper
 
getInt_parameters() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryPluginRunner
 
getInt_parameters() - Method in interface com.github.seqware.queryengine.plugins.MapperInterface
 
getInternalParameters() - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
 
getInternalParameters() - Method in interface com.github.seqware.queryengine.plugins.PluginInterface
 
getInternalParameters() - Method in class com.github.seqware.queryengine.plugins.plugins.FeatureSetCountPlugin
getInternalParameters() - Method in class com.github.seqware.queryengine.plugins.plugins.VCFDumperPlugin
getInvitationCode() - Method in class net.sourceforge.seqware.common.model.Registration
Getter for the field invitationCode.
getInvoice() - Method in class net.sourceforge.seqware.common.model.Expense
Getter for the field invoice.
getInvoiceId() - Method in class net.sourceforge.seqware.common.model.Invoice
Getter for the field invoiceId.
getInvoiceService() - Method in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController
Getter for the field invoiceService.
getInvoiceService() - Method in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController
Getter for the field invoiceService.
getIsEnd() - Method in class net.sourceforge.solexatools.util.PageInfo
Getter for the field isEnd.
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field isHasFile.
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.IUS
Getter for the field isHasFile.
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field isHasFile.
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field isHasFile.
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field isHasFile.
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field isHasFile.
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field isHasFile.
getIsInvitationCode() - Method in class net.sourceforge.seqware.common.invitation.InvitationParams
Getter for the field isInvitationCode.
getIsSelected() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field isSelected.
getIsSelected() - Method in class net.sourceforge.seqware.common.model.File
Getter for the field isSelected.
getIsSelected() - Method in class net.sourceforge.seqware.common.model.IUS
Getter for the field isSelected.
getIsSelected() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field isSelected.
getIsSelected() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field isSelected.
getIsSelected() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field isSelected.
getIsSelected() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field isSelected.
getIsSelected() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field isSelected.
getIsStart() - Method in class net.sourceforge.solexatools.util.PageInfo
Getter for the field isStart.
getItemRgb() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Getter for the field itemRgb.
getIus() - Method in class net.sourceforge.seqware.common.model.FileReportRow
Getter for the field ius.
getIus() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
Getter for the field ius.
getIus() - Method in class net.sourceforge.seqware.common.model.IUSLink
Getter for the field ius.
getIus() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field ius.
getIUS() - Method in class net.sourceforge.seqware.common.model.Lane
getIUS.
getIUS() - Method in class net.sourceforge.seqware.common.model.Processing
getIUS.
getIus() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
Getter for the field ius.
getIUS() - Method in class net.sourceforge.seqware.common.model.Sample
getIUS.
getIus() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
Getter for the field ius.
getIus() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
Getter for the field ius.
getIus() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field ius.
getIus() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem
Getter for the field ius.
getIus() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
Getter for the field ius.
getIusAttributeId() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
Getter for the field iusAttributeId.
getIusAttributes() - Method in class net.sourceforge.seqware.common.model.IUS
Getter for the field iusAttributes.
getIusFiles() - Method in interface net.sourceforge.seqware.webservice.resources.tables.IusFilesResource
List files associated with Ius.
getIusFiles() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusFilesServerResource
List files associated with Ius.
getIUSFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getIUSFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
Get IUSes (barcodes) from a lane or sample.
getIUSFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getIUSFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getIUSHtml(IUS, Registration, String, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
getIUSHtml.
getIusId() - Method in class net.sourceforge.seqware.common.model.IUS
Getter for the field iusId.
getIusLinkId() - Method in class net.sourceforge.seqware.common.model.IUSLink
Getter for the field iusLinkId.
getIusLinks() - Method in class net.sourceforge.seqware.common.model.IUS
Getter for the field iusLinks.
getIusService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field iusService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
Getter for the field iusService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
getIUSService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
Getter for the field iusService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
getIUSService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.IUSSetupController
Getter for the field iusService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
Getter for the field iusService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
getIUSService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
Getter for the field iusService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
getIUSService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
Getter for the field iusService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
getIUSService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
Getter for the field iusService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
getIUSService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
Getter for the field iusService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
getIUSService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
getIUSService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Getter for the field iusService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
getIUSService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
Getter for the field iusService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
getIUSService.
getIUSServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getIUSServiceBean.
getIusSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getIusSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getIusTag() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getJavaElement() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJavaJob
FIXME: this is untested, not sure if it will work!
getJavaElement() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
getJavaElement() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob
 
getJobObject() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
getJobObject() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
getJobs() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
get all jobs in current workflow
getJoinDevelopersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration
Getter for the field joinDevelopersMailingList.
getJoinUsersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration
Getter for the field joinUsersMailingList.
getJsonEscapeAlgorithm() - Method in class net.sourceforge.seqware.common.model.Processing
getJsonEscapeAlgorithm.
getJsonEscapeDefaultValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
getJsonEscapeDefaultValue.
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Experiment
getJsonEscapeDescription.
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.File
getJsonEscapeDescription.
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.IUS
getJsonEscapeDescription.
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Lane
getJsonEscapeDescription.
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Processing
getJsonEscapeDescription.
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Sample
getJsonEscapeDescription.
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.SequencerRun
getJsonEscapeDescription.
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Study
getJsonEscapeDescription.
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Workflow
getJsonEscapeDescription.
getJsonEscapeDescription200() - Method in class net.sourceforge.seqware.common.model.Experiment
getJsonEscapeDescription200.
getJsonEscapeDescription200() - Method in class net.sourceforge.seqware.common.model.Study
getJsonEscapeDescription200.
getJsonEscapeDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
getJsonEscapeDisplayName.
getJsonEscapeDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
getJsonEscapeDisplayName.
getJsonEscapeFileName() - Method in class net.sourceforge.seqware.common.model.File
getJsonEscapeFileName.
getJsonEscapeFullName() - Method in class net.sourceforge.seqware.common.model.Workflow
getJsonEscapeFullName.
getJsonEscapeKey() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
getJsonEscapeKey.
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Experiment
getJsonEscapeName.
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.IUS
getJsonEscapeName.
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Lane
getJsonEscapeName.
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Sample
getJsonEscapeName.
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.SequencerRun
getJsonEscapeName.
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Workflow
getJsonEscapeName.
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
getJsonEscapeName.
getJsonEscapeTitle() - Method in class net.sourceforge.seqware.common.model.Experiment
getJsonEscapeTitle.
getJsonEscapeTitle() - Method in class net.sourceforge.seqware.common.model.Sample
getJsonEscapeTitle.
getJsonEscapeTitle() - Method in class net.sourceforge.seqware.common.model.Study
getJsonEscapeTitle.
getJsonEscapeType() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
getJsonEscapeType.
getJsonEscapeValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
getJsonEscapeValue.
getJsonEscapeValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
getJsonEscapeValue.
getJSONFeature(String, String) - Method in class com.github.seqware.queryengine.system.rest.resources.FeatureSetResource
Return a specific feature in JSON
getKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getKey() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getKey() - Method in class com.github.seqware.queryengine.model.Tag
Get the key.
getKey() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Getter for the field key.
getKey() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
Getter for the field key.
getKey() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
Getter for the field key.
getKey() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
Getter for the field key.
getKeyIndex() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Getter for the field keyIndex.
getKeyValueFromFile(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
getKeyValueFromFile.
getKeyvalues() - Method in class net.sourceforge.seqware.queryengine.backend.model.Model
Getter for the field keyvalues.
getLabel() - Method in class net.sourceforge.seqware.common.model.ExperimentLink
Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.IUSLink
Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.LaneLink
Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.SampleLink
Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.StudyLink
Getter for the field label.
getLABEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
Gets the value of the label property.
getLABEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
Gets the value of the label property.
getLABEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK
Gets the value of the label property.
getLABEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
Gets the value of the label property.
getLABEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK
Gets the value of the label property.
getLabName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the labName property.
getLane() - Method in class net.sourceforge.seqware.common.model.FileReportRow
Getter for the field lane.
getLane() - Method in class net.sourceforge.seqware.common.model.IUS
Getter for the field lane.
getLane() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
Getter for the field lane.
getLane() - Method in class net.sourceforge.seqware.common.model.LaneLink
Getter for the field lane.
getLane() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
Getter for the field lane.
getLane() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
Getter for the field lane.
getLane() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
Getter for the field lane.
getLane() - Method in class net.sourceforge.seqware.common.model.ShareLane
Getter for the field lane.
getLane() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Get the value of lane
getLane() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
getLane() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem
Getter for the field lane.
getLane1() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field lane1.
getLane2() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field lane2.
getLane3() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field lane3.
getLane4() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field lane4.
getLane5() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field lane5.
getLane6() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field lane6.
getLane7() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field lane7.
getLane8() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field lane8.
getLane_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Getter for the field lane_url.
getLaneAttributeId() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
Getter for the field laneAttributeId.
getLaneAttributes() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field laneAttributes.
getLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
Getter for the field laneCount.
getLaneHtml(Lane, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
getLaneHtml.
getLaneHtml(Lane, Registration, Integer) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
getLaneHtml.
getLaneId() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field laneId.
getLaneIndex() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field laneIndex.
getLaneLinkId() - Method in class net.sourceforge.seqware.common.model.LaneLink
Getter for the field laneLinkId.
getLaneLinks() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field laneLinks.
getLaneName() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getLanes() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field lanes.
getLanes() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field lanes.
getLanes() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field lanes.
getLanes() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field lanes.
getLanes() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field lanes.
getLaneService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.validation.LaneValidator
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSetupController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
Getter for the field laneService.
getLaneServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getLaneServiceBean.
getLanesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getLanesFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
Get Lanes from a sequencer run.
getLanesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getLanesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getLaneSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getLaneSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getLastName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getLastName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getLastName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getLastName() - Method in class com.github.seqware.queryengine.model.User
Get last name
getLastName() - Method in class net.sourceforge.seqware.common.model.Registration
Getter for the field lastName.
getLastName() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
Getter for the field lastName.
getLatestAtomByRowKey(String, Class<T>) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
Find an atom in the back-end when a specific class is known and a specific row key is known
getLatestAtomByRowKey(String, Class<T>) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Find an atom in the back-end when a specific class is known and a specific row key is known
getLatestAtomBySGID(SGID) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
Find the latest object in the back-end by a globally unique SGID while ignoring the timestamp
getLatestAtomBySGID(SGID, Class<T>) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
Find an object in the back-end when a specific class is known while ignoring the timestamp
getLatestAtomBySGID(SGID) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Deprecated. It is much more efficient to retrieve an Atom when you know the class
getLatestAtomBySGID(SGID, Class<T>) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Find an object in the back-end when a specific class is known while ignoring the timestamp
getLatestModel(String, TupleBinding, HTable, String, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
This is actually a pretty dangerous method since just the most recent biallelic variant will be returned.
getLayout() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Getter for the field layout.
getLeastSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
getLeastSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
getLeastSigBits() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
 
getLength() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Getter for the field length.
getLibraries() - Method in class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl
Returns a complete list of libraries.
getLibraries(Map<String, String>) - Method in class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl
Returns a list of libraries that match all attributes provided in the give attributes Map.
getLibraries() - Method in interface net.sourceforge.seqware.common.business.LibraryService
Returns a complete list of libraries.
getLibraries(Map<String, String>) - Method in interface net.sourceforge.seqware.common.business.LibraryService
Returns a list of libraries that match all attributes provided in the give attributes Map.
getLibraries(String, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate
Returns list of libraries that contain the attribute attributeName=attributeValue.
getLibraries() - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate
Returns a complete list of libraries.
getLibraries(String, String) - Method in interface net.sourceforge.seqware.common.dao.LibraryDAO
Returns list of libraries that contain the attribute attributeName=attributeValue.
getLibraries() - Method in interface net.sourceforge.seqware.common.dao.LibraryDAO
Returns a complete list of libraries.
getLibraries() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrariesResource
getLibraries.
getLIBRARYCONSTRUCTIONPROTOCOL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Gets the value of the libraryconstructionprotocol property.
getLIBRARYDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
Gets the value of the librarydescriptor property.
getLibraryId() - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto
Getter for the field libraryId.
getLIBRARYLAYOUT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Gets the value of the librarylayout property.
getLIBRARYNAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Gets the value of the libraryname property.
getLibrarySamples() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
Getter for the field librarySamples.
getLibrarySelection() - Method in class net.sourceforge.seqware.common.model.Lane
 
getLIBRARYSELECTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Gets the value of the libraryselection property.
getLibrarySelectionId() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
Getter for the field librarySelectionId.
getLibrarySelections() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getLibrarySelections() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getLibrarySelections.
getLibrarySelections() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getLibrarySelections() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getLibrarySelectionService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getLibrarySelectionService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Getter for the field librarySelectionService.
getLibrarySelectionService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
Getter for the field librarySelectionService.
getLibrarySelectionServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getLibrarySelectionServiceBean.
getLibraryService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field libraryService.
getLibraryServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getLibraryServiceBean.
getLibrarySource() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getLibrarySource() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getLibrarySource.
getLibrarySource() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getLibrarySource() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getLibrarySource() - Method in class net.sourceforge.seqware.common.model.Lane
 
getLIBRARYSOURCE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Gets the value of the librarysource property.
getLibrarySourceId() - Method in class net.sourceforge.seqware.common.model.LibrarySource
Getter for the field librarySourceId.
getLibrarySourceService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getLibrarySourceService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Getter for the field librarySourceService.
getLibrarySourceService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
Getter for the field librarySourceService.
getLibrarySourceServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getLibrarySourceServiceBean.
getLibraryStrategies() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getLibraryStrategies() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getLibraryStrategies.
getLibraryStrategies() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getLibraryStrategies() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getLibraryStrategy() - Method in class net.sourceforge.seqware.common.model.Lane
 
getLIBRARYSTRATEGY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Gets the value of the librarystrategy property.
getLibraryStrategyId() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
Getter for the field libraryStrategyId.
getLibraryStrategyService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getLibraryStrategyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Getter for the field libraryStrategyService.
getLibraryStrategyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
Getter for the field libraryStrategyService.
getLibraryStrategyServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getLibraryStrategyServiceBean.
getLibraryType() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
Getter for the field libraryType.
getList() - Method in class net.sourceforge.seqware.common.model.lists.ExperimentList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.FileList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.IUSList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.LaneList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.LibrarySelectionList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.LibrarySourceList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.LibraryStrategyList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.OrganismList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.PlatformList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.ProcessingList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.ReturnValueList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.SampleList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.SequencerRunList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.StudyList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.StudyTypeList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList
getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2
getList.
getLocalhost(OptionSet) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
Get the localhost and a return value describing the failure condition if we are unable to get the localhost
getLocatableModels(SecondaryDatabase, TupleBinding, String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getLocatableModels.
getLocatableModels(String, String, TupleBinding, String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getLocatableModels.
getLock() - Method in class com.github.seqware.queryengine.system.importers.Importer
getLock.
getLock() - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
Deprecated. Lock file, do not clear on exit
getLock(boolean) - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
Deprecated. Lock file, but give option to free lock when the JVM exits.
getLock(int, int) - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
Deprecated. getLock.
getLock() - Method in class net.sourceforge.seqware.queryengine.tools.importers.Importer
getLock.
getLongName() - Method in class net.sourceforge.seqware.common.model.Platform
getLongName.
getLS454() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
Gets the value of the ls454 property.
getMainClass() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
return the main class for a Java job, or the script.pl for a perl Job
getManager() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Get the model manager for this Atom
getMap() - Method in class com.github.seqware.queryengine.util.obo.OboFileHandlerHack
Getter for the field map.
getMapOutputKeyClass() - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
 
getMapOutputKeyClass() - Method in class com.github.seqware.queryengine.plugins.plugins.VCFDumperPlugin
 
getMapOutputValueClass() - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
 
getMapOutputValueClass() - Method in class com.github.seqware.queryengine.plugins.plugins.VCFDumperPlugin
 
getMapperClass() - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
 
getMapred_job_tracker() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getMaxCoverage() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Getter for the field maxCoverage.
getMaxCoverage() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Getter for the field maxCoverage.
getMaxCoverage() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Getter for the field maxCoverage.
getMaximumMappingQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field maximumMappingQuality.
getMaxLockers() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Getter for the field maxLockers.
getMaxLockObjects() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Getter for the field maxLockObjects.
getMaxLocks() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Getter for the field maxLocks.
getMaxMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
getMaxMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
 
getMaxMemory() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getMD5Hash(String) - Method in class net.sourceforge.seqware.common.metadata.Metadata
getMD5Hash.
getMd5sum() - Method in class net.sourceforge.seqware.common.model.File
Getter for the field md5sum.
getMd5sum() - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
getMd5sum() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
getMd5sum() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
Getter for the field md5sum.
getMeaning() - Method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus
 
getMEMBER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF
Gets the value of the member property.
getMEMBER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS
Gets the value of the member property.
getMEMBERS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Gets the value of the members property.
getMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getMemReq() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Getter for the field memReq.
getMetadata() - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
Getter for the field metadata.
getMetadata() - Method in class net.sourceforge.seqware.pipeline.module.Module
Getter for the field metadata.
getMetadata() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
 
getMetadata() - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
getMetadata.
getMetadata(long) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
getMetadata.
getMetadata_output_dir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getMetadata_output_file_prefix() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getMetadataOutputPrefix() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob
 
getMetadataOutputPrefix() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob
 
getMetadataWriteback() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
getMetaType() - Method in class net.sourceforge.seqware.common.model.File
Getter for the field metaType.
getMetaType() - Method in class net.sourceforge.seqware.common.model.FileType
Getter for the field metaType.
getMetaType() - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
getMetaType() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
getMetaType() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
Getter for the field metaType.
getMimeType() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
getMinCoverage() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Getter for the field minCoverage.
getMinCoverage() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Getter for the field minCoverage.
getMinCoverage() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Getter for the field minCoverage.
getMinObservations() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Getter for the field minObservations.
getMinObservationsPerStrand() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Getter for the field minObservationsPerStrand.
getMinPercent() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Getter for the field minPercent.
getMinSnpQuality() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Getter for the field minSnpQuality.
getMinSnpQuality() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Getter for the field minSnpQuality.
getMinSNVPhred() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Getter for the field minSNVPhred.
getMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getMismatch.
getMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getMismatch.
getMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getMismatch.
getMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getMismatch.
getMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getMismatch.
getMismatch(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getMismatch.
getMismatchAAChangeBlosumScore() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field mismatchAAChangeBlosumScore.
getMismatchAminoAcidChange() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field mismatchAminoAcidChange.
getMismatchChr() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field mismatchChr.
getMismatchCodonChange() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field mismatchCodonChange.
getMismatchCodonPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field mismatchCodonPosition.
getMismatches() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getMismatches.
getMismatches(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getMismatches.
getMismatches(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getMismatches.
getMismatches() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getMismatches.
getMismatches(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getMismatches.
getMismatches(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getMismatches.
getMismatches() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getMismatches.
getMismatches(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getMismatches.
getMismatches(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getMismatches.
getMismatches() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getMismatches.
getMismatches(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getMismatches.
getMismatches(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getMismatches.
getMismatches() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getMismatches.
getMismatches(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getMismatches.
getMismatches(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getMismatches.
getMismatches() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getMismatches.
getMismatches(String, int, int) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getMismatches.
getMismatches(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getMismatches.
getMismatches() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication
Getter for the field mismatches.
getMismatches() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion
Getter for the field mismatches.
getMismatchesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getMismatchesByTag.
getMismatchesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getMismatchesByTag.
getMismatchesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getMismatchesByTag.
getMismatchesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getMismatchesByTag.
getMismatchesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getMismatchesByTag.
getMismatchesByTag(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getMismatchesByTag.
getMismatchesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
Get access to an iterator containing all the mismatch tags.
getMismatchesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getMismatchesTags.
getMismatchesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
Get access to an iterator containing all the mismatch tags.
getMismatchesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
Get access to an iterator containing all the mismatch tags.
getMismatchesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getMismatchesTags.
getMismatchesTags() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getMismatchesTags.
getMismatchesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getMismatchesUnordered.
getMismatchesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getMismatchesUnordered.
getMismatchesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getMismatchesUnordered.
getMismatchesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getMismatchesUnordered.
getMismatchesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getMismatchesUnordered.
getMismatchesUnordered() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getMismatchesUnordered.
getMismatchId() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field mismatchId.
getMismatchStart() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field mismatchStart.
getMismatchStop() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field mismatchStop.
getMismatchTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getMismatchTagsBySearch.
getMismatchTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getMismatchTagsBySearch.
getMismatchTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
getMismatchTagsBySearch.
getMismatchTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getMismatchTagsBySearch.
getMismatchTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
getMismatchTagsBySearch.
getMismatchType() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field mismatchType.
getModel(String, TupleBinding, HTable, String, String, Long) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getModel.
getModel(String, String, String, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getModel.
getModelAndView(String, ModelAndView) - Static method in class net.sourceforge.solexatools.util.StudyBuildTree
getModelAndView.
getModelClass() - Method in class com.github.seqware.queryengine.system.rest.resources.FeatureSetResource
 
getModelClass() - Method in class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
Class of the elements in the set, used for casting and type-check operations
getModelClass() - Method in class com.github.seqware.queryengine.system.rest.resources.GroupResource
 
getModelClass() - Method in class com.github.seqware.queryengine.system.rest.resources.PluginResource
 
getModelClass() - Method in class com.github.seqware.queryengine.system.rest.resources.PluginRunResource
 
getModelClass() - Method in class com.github.seqware.queryengine.system.rest.resources.ReferenceResource
 
getModelClass() - Method in class com.github.seqware.queryengine.system.rest.resources.ReferenceSetResource
 
getModelClass() - Method in class com.github.seqware.queryengine.system.rest.resources.TagResource
 
getModelClass() - Method in class com.github.seqware.queryengine.system.rest.resources.TagSetResource
 
getModelClass() - Method in class com.github.seqware.queryengine.system.rest.resources.UserResource
 
getModelManager() - Static method in class com.github.seqware.queryengine.factory.SWQEFactory
Return a new model manager to create and keep track of entities
getModels(SecondaryDatabase, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getModels.
getModels(HTable, Filter, TupleBinding, String, String, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getModels.
getModels(HTable, Scan, Filter, TupleBinding, String, String, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getModels.
getModels(String, String, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getModels.
getModelsByTag(SecondaryDatabase, TupleBinding, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getModelsByTag.
getModelsByTag(String, HTable, HTable, TupleBinding, String, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
getModelsByTag.
getModelsByTag(String, String, String, String, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getModelsByTag.
getModelsTags(SecondaryDatabase, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
Get access to an iterator containing all the mismatch tags.
getModelsTags(String, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getModelsTags.
getModelsTags(String, String, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getModelsTags.
getModelsUnordered(Database, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
getModelsUnordered.
getModelsUnordered(String, String, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
getModelsUnordered.
getModelTags(HTable) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
Other methods expect this to return a SeqWareIterator and not a HashMap.
getMODIFY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Gets the value of the modify property.
getModuleType() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
Getter for the field moduleType.
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginPBOrBuilder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginRunPBOrBuilder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginPBOrBuilder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginRunPBOrBuilder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getMostSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
getMostSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
getMostSigBits() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
 
getMULTIPLIER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
Gets the value of the multiplier property.
getMutatedGenomicSequence() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field mutatedGenomicSequence.
getMutatedTranslatedSequence() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field mutatedTranslatedSequence.
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
getName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginPBOrBuilder
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getName() - Method in class com.github.seqware.queryengine.kernel.RPNStack.Parameter
 
getName() - Method in interface com.github.seqware.queryengine.model.Group
Get the name of the group
getName() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
Get the name of the group
getName() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryPlugin
Get the name of the plugin
getName() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference
The name of this reference (ex: "hg 19")
getName() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet
Get the name of the reference set
getName() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
Get the name of the tag set
getName() - Method in interface com.github.seqware.queryengine.model.Plugin
Get the name of the plugin
getName() - Method in interface com.github.seqware.queryengine.model.Reference
The name of this reference (ex: "hg 19")
getName() - Method in interface com.github.seqware.queryengine.model.ReferenceSet
Get the name of the reference set
getName() - Method in interface com.github.seqware.queryengine.model.TagSet
Get the name of the tag set
getName() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.IUS
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.LibrarySource
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.Organism
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.Platform
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.Project
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.StudyType
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Get the value of name
getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
 
getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
getName.
getName() - Method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Module
getName.
getName() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Gets the value of the name property.
getName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
Gets the value of the name property.
getName() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Getter for the field name.
getName() - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto
Getter for the field name.
getName() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
getNameNode() - Method in class net.sourceforge.seqware.common.business.UploadFile
Getter for the field nameNode.
getNamespace() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
 
getNamespace() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
getNamespace.
getNamespace() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
 
getNcbiTaxId() - Method in class net.sourceforge.seqware.common.model.Organism
Getter for the field ncbiTaxId.
getNcbiTaxonomyId() - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto
Getter for the field ncbiTaxonomyId.
getNestedTags(TagSet) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Convenience method for getNestedTags(String tagSet)
getNestedTags(String) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Get tags that have been sorted into a structure of Nested Maps.
getNestedTags(String) - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable
Get tags that have been sorted into a structure of Nested Maps.
getNestedTags(TagSet) - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable
Convenience method for getNestedTags(String tagSet)
getNetwork() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getNetworkReq() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Getter for the field networkReq.
getNewStudyType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE
Gets the value of the newStudyType property.
getNewType() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field newType.
getNodeHtml(Processing, Registration, String, boolean, boolean, boolean, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
getNodeHtml.
getNodeHtml(Processing, Registration) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
getNodeHtml.
getNodeIds(Object) - Static method in class net.sourceforge.solexatools.util.FindChildUtil
getNodeIds.
getNominalLength() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Getter for the field nominalLength.
getNOMINALLENGTH() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
Gets the value of the nominallength property.
getNominalSdev() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Getter for the field nominalSdev.
getNOMINALSDEV() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
Gets the value of the nominalsdev property.
getNotes() - Method in class net.sourceforge.seqware.common.model.Invoice
Getter for the field notes.
getNotes() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
Gets the value of the notes property.
getNotes() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
Gets the value of the notes property.
getNotes() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
Gets the value of the notes property.
getNotes() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE
Gets the value of the notes property.
getNotes() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS
Gets the value of the notes property.
getNotes() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
Gets the value of the notes property.
getNotRunned() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Getter for the field notRunned.
getNumber() - Method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
getNumberChannels() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Gets the value of the numberChannels property.
getNUMBEROFLEVELS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
Gets the value of the numberoflevels property.
getNUMBEROFREADSPERSPOT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
Gets the value of the numberofreadsperspot property.
getNumQueries() - Method in interface com.github.seqware.queryengine.system.exporters.QueryDumperInterface
Return the number of queries that we wish to run consecutively
getNumReduceTasks() - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
 
getNumReduceTasks() - Method in class com.github.seqware.queryengine.plugins.plugins.VCFDumperPlugin
 
getOffspringProcessings() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field offspringProcessings.
getOkTo() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
getOOZIE_APP_PATH() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getOOZIE_APP_ROOT() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getOOZIE_JOBTRACKER() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getOOZIE_NAMENODE() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getOOZIE_QUEUENAME() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getOOZIE_URL() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getOOZIE_WORK_DIR() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getOozieWorkingDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.module.Module
getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory
 
getOrganism() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getOrganism() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getOrganism() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getOrganism() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet
Get the organism associated with this reference set
getOrganism() - Method in interface com.github.seqware.queryengine.model.ReferenceSet
Get the organism associated with this reference set
getOrganism() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field organism.
getOrganism() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field organism.
getOrganism() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Get the value of organism
getOrganism() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Getter for the field organism.
getOrganismId() - Method in class net.sourceforge.seqware.common.model.Organism
Getter for the field organismId.
getOrganismId() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field organismId.
getOrganisms() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getOrganisms() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getOrganisms.
getOrganisms() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getOrganisms() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getOrganismService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getOrganismService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
Getter for the field organismService.
getOrganismService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
Getter for the field organismService.
getOrganismServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getOrganismServiceBean.
getORIENTATION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
Gets the value of the orientation property.
getOriginalFileName() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Getter for the field originalFileName.
getOs() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
 
getOutput() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
Getter for the field output.
getOutputClass() - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
 
getOutputClass() - Method in interface com.github.seqware.queryengine.plugins.PluginInterface
 
getOutputClass() - Method in class com.github.seqware.queryengine.plugins.plugins.FeaturesByFilterPlugin
 
getOutputClass() - Method in class com.github.seqware.queryengine.plugins.plugins.FeatureSetCountPlugin
 
getOutputDir() - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
Getter for the field outputDir.
getOutputDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob
 
getOutputDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob
 
getOutputFilename() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
Getter for the field outputFilename.
getOutputFilename() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Getter for the field outputFilename.
getOutputFiles() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
Getter for the field outputFiles.
getOutputPath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
 
getOwner() - Method in class com.github.seqware.queryengine.model.interfaces.ACL
Get the owner for the object
getOwner() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.File
Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.Invoice
Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.IUS
Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Getter for the field owner.
getOwnerId() - Method in class net.sourceforge.seqware.common.model.Project
Getter for the field ownerId.
getOwnerSGID() - Method in class com.github.seqware.queryengine.model.interfaces.ACL
Get the owner for the object
getOwnerUserName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getPage() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
Getter for the field page.
getPageInfo(HttpServletRequest, String, List, List, String, String, MessageSourceAccessor) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
getPageInfo.
getPageInfoSD(HttpServletRequest, String, List, List, MessageSourceAccessor) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
getPageInfoSD.
getPageNumber(HttpServletRequest, Study, List<Study>) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
getPageNumber.
getPaidAmount() - Method in class net.sourceforge.seqware.common.model.Invoice
Getter for the field paidAmount.
getPAIRED() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
Gets the value of the paired property.
getPairedEnd() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field pairedEnd.
getPairedEnd() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field pairedEnd.
getPairedFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field pairedFilePath.
getPairedFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field pairedFilePath.
getPairedOrientation() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Getter for the field pairedOrientation.
getParameters() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
getParameters() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
getParameters() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginRunPBOrBuilder
 
getParameters() - Method in class com.github.seqware.queryengine.kernel.RPNStack
Returns the parameters of the argument stack, i.e., everything that is not a constant and considered to be a variable.
getParameters() - Method in class com.github.seqware.queryengine.model.PluginRun
Get the parameters for this particular creation of an pluginRun plug-in
getParameters() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field parameters.
getParameters() - Method in class net.sourceforge.seqware.common.module.ReturnValue
Getter for the field parameters.
getParameters() - Method in class net.sourceforge.seqware.pipeline.module.Module
Getter for the field parameters.
getParams() - Method in class net.sourceforge.solexatools.util.SummaryLine
Getter for the field params.
getPARENT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the parent property.
getParentAccessions() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getParentAccessions() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
getParentAccessions() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
 
getParentId() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy
 
getParentLane(Processing, Integer) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
getParentLane.
getParentProcessing(Processing, Integer) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
getParentProcessing.
getParentProcessingAccession() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
Getter for the field parentProcessingAccession.
getParentProcessings() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
Getter for the field parentProcessings.
getParents() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field parents.
getParents() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field parents.
getParents() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
getParents() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
getParents() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
add all parent jobs
getParents() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getParentSample() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Get the value of parentSample
getParentSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getParentSamplesFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
Get the parent samples of a sample.
getParentSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getParentSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getParentUrls() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Getter for the field parentUrls.
getParentWorkflowAccessions() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
getPassword() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getPassword() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getPassword() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getPassword() - Method in class com.github.seqware.queryengine.model.User
A hashed password for the user
getPassword() - Method in class net.sourceforge.seqware.common.model.Registration
Getter for the field password.
getPassword() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Getter for the field password.
getPasswordHint() - Method in class net.sourceforge.seqware.common.model.Registration
Getter for the field passwordHint.
getPathToFirstFile() - Method in class net.sourceforge.seqware.common.model.UploadSequence
Getter for the field pathToFirstFile.
getPathToSecondFile() - Method in class net.sourceforge.seqware.common.model.UploadSequence
Getter for the field pathToSecondFile.
getPeakMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getPeakThreads() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getPegasusConfigDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getPending() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Getter for the field pending.
getPermanentBundleLocation() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field permanentBundleLocation.
getPermBundleLocation() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Getter for the field permBundleLocation.
getPermissions() - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl
Get permissions for the subject.
getPermissions() - Method in interface com.github.seqware.queryengine.model.interfaces.ACLable
Get permissions for the subject.
getPfn() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
 
getPhase() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getPhase() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getPhase() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getPhase() - Method in class com.github.seqware.queryengine.model.Feature
(GVF: The phase column is not used in GVF, but is maintained with the placeholder '.' (period) for compatibility with GFF3 and tools that conform to the GFF3 specification (and do change it))
getPipelineJarPath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Adag
 
getPlatform() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field platform.
getPlatform() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field platform.
getPlatform() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field platform.
getPLATFORM() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the platform property.
getPlatformId() - Method in class net.sourceforge.seqware.common.model.Platform
Getter for the field platformId.
getPlatformInt() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field platformInt.
getPlatformInt() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field platformInt.
getPlatforms() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getPlatforms() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getPlatforms.
getPlatforms() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getPlatforms() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getPlatformService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field platformService.
getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Getter for the field platformService.
getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
Getter for the field platformService.
getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Getter for the field platformService.
getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
Getter for the field platformService.
getPlatformServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getPlatformServiceBean.
getPlugin() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner
 
getPlugin() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryPluginRunner
 
getPlugin() - Method in interface com.github.seqware.queryengine.plugins.PluginRunnerInterface
 
getPluginInterfaces() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
getPluginInterfaces.
getPluginInterfaces() - Method in interface com.github.seqware.queryengine.model.QueryInterface
getPluginInterfaces.
getPluginRunIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getPluginRunIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
getPluginRunIDs(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginPBOrBuilder
 
getPluginRunIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getPluginRunIDsBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getPluginRunIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getPluginRunIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
getPluginRunIDsCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginPBOrBuilder
 
getPluginRunIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getPluginRunIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
getPluginRunIDsList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginPBOrBuilder
 
getPluginRunIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getPluginRunIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
getPluginRunIDsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginPBOrBuilder
 
getPluginRunIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getPluginRunIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
getPluginRunIDsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginPBOrBuilder
 
getPluginRunner(PluginInterface, FeatureSet, Object...) - Static method in class com.github.seqware.queryengine.factory.SWQEFactory
 
getPluginRunner() - Method in class com.github.seqware.queryengine.model.PluginRun
Get pluginRun plugin
getPluginRuns() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
getPluginRuns.
getPluginRuns() - Method in interface com.github.seqware.queryengine.model.QueryInterface
getPluginRuns.
getPlugins() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd
getPlugins.
getPlugins() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
getPlugins.
getPlugins() - Method in interface com.github.seqware.queryengine.model.QueryInterface
getPlugins.
getPmi() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Getter for the field pmi.
getPmi() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Getter for the field pmi.
getPostgresqlPersistenceStrategy() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Getter for the field postgresqlPersistenceStrategy.
getPragma() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getPragma() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getPragma() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getPragma() - Method in class com.github.seqware.queryengine.model.Feature
GVF provides pragmas that are file-wide.
getPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getPrecedingID() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getPrecedingID() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getPrecedingIDBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getPrecedingIDBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getPrecedingIDOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getPrecedingIDOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getPrecedingIDOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getPrecedingIDOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getPrecedingIDOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getPrecedingIDOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getPrecedingSGID() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Used in back-end to get previous version ID
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginPBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginRunPBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getPrecedingVersion() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Returns the subject (if any) that represents a previous version.
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.model.interfaces.Versionable
Returns the subject (if any) that represents a previous version.
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginPBOrBuilder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginRunPBOrBuilder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
getPredicate() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getPredicate() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getPredicate() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getPredicate() - Method in class com.github.seqware.queryengine.model.Tag
Get the predicate.
getPricePerUnit() - Method in class net.sourceforge.seqware.common.model.Expense
Getter for the field pricePerUnit.
getPricePerUnitString() - Method in class net.sourceforge.seqware.common.model.Expense
Getter for the field pricePerUnit.
getPrivate() - Method in class net.sourceforge.seqware.common.model.Workflow
getPrivate.
getProcess() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field process.
getProcessedCnt(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
getProcessedCnt.
getProcessedCnt(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
getProcessedCnt.
getProcessedCnt() - Method in class net.sourceforge.seqware.common.model.Lane
getProcessedCnt.
getProcessedCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRun
getProcessedCnt.
getProcessedCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field processedCount.
getProcessExitStatus() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field processExitStatus.
getProcessExitStatus() - Method in class net.sourceforge.seqware.common.module.ReturnValue
Getter for the field processExitStatus.
getProcessing() - Method in class net.sourceforge.seqware.common.model.FileReportRow
Getter for the field processing.
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
Getter for the field processing.
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
Getter for the field processing.
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
Getter for the field processing.
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
Getter for the field processing.
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
Getter for the field processing.
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
Getter for the field processing.
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
Getter for the field processing.
getProcessing() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
Getter for the field processing.
getPROCESSING() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the processing property.
getProcessingAccession() - Method in class net.sourceforge.seqware.pipeline.module.Module
Getter for the field processingAccession.
getProcessingAttributeId() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
Getter for the field processingAttributeId.
getProcessingAttributes() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field processingAttributes.
getProcessingByChildId() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
Getter for the field processingByChildId.
getProcessingByParentId() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
Getter for the field processingByParentId.
getProcessingCnt(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
getProcessingCnt.
getProcessingCnt(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
getProcessingCnt.
getProcessingCnt() - Method in class net.sourceforge.seqware.common.model.Lane
getProcessingCnt.
getProcessingCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRun
getProcessingCnt.
getProcessingCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
getProcessingCnt.
getProcessingCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field processingCount.
getProcessingExperimentServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getProcessingExperimentServiceBean.
getProcessingExperimentsId() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
Getter for the field processingExperimentsId.
getProcessingExperimentsService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field processingExperimentsService.
getProcessingHtml(Processing, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
getProcessingHtml.
getProcessingId() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field processingId.
getProcessingIusId() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
Getter for the field processingIusId.
getProcessingIusService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field processingIusService.
getProcessingIUSServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getProcessingIUSServiceBean.
getProcessingLaneService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field processingLaneService.
getProcessingLaneServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getProcessingLaneServiceBean.
getProcessingLanesId() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
Getter for the field processingLanesId.
getProcessingRelations(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getProcessingRelations(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getProcessingRelations.
getProcessingRelations(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getProcessingRelations(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getProcessingRelationshipId() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
Getter for the field processingRelationshipId.
getProcessingRelationshipService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field processingRelationshipService.
getProcessingRelationshipServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getProcessingRelationshipServiceBean.
getProcessings() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field processings.
getProcessings() - Method in class net.sourceforge.seqware.common.model.File
Getter for the field processings.
getProcessings() - Method in class net.sourceforge.seqware.common.model.IUS
Getter for the field processings.
getProcessings() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field processings.
getProcessings() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field processings.
getProcessings() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field processings.
getProcessings() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field processings.
getProcessings() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field processings.
getProcessings() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field processings.
getProcessingSampleServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getProcessingSampleServiceBean.
getProcessingSamplesId() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
Getter for the field processingSamplesId.
getProcessingSamplesService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field processingSamplesService.
getProcessingsByWorkflow(WorkflowRun) - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
getProcessingsByWorkflow.
getProcessingSequencerRunService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field processingSequencerRunService.
getProcessingSequencerRunsId() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
Getter for the field processingSequencerRunsId.
getProcessingSequencerRunsServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getProcessingSequencerRunsServiceBean.
getProcessingService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
Getter for the field processingService.
getProcessingServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getProcessingServiceBean.
getProcessingStudiesId() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
Getter for the field processingStudiesId.
getProcessingStudiesService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field processingStudiesService.
getProcessingStudiesServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getProcessingStudiesServiceBean.
getProcStatuses(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
getProcStatuses.
getProcStatuses(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
getProcStatuses.
getProjectId() - Method in class net.sourceforge.seqware.common.model.Project
Getter for the field projectId.
getProjectId() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field projectId.
getPROJECTID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Gets the value of the projectid property.
getProperty(String) - Static method in class net.sourceforge.seqware.common.util.configtools.ConfigTools
getProperty.
getProperty(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
get the user defined INI files properties
getProperty(String) - Static method in class net.sourceforge.seqware.queryengine.webservice.util.EnvUtil
getProperty.
getPROTECT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Gets the value of the protect property.
getProvisionedPath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
 
getPublic() - Method in class net.sourceforge.seqware.common.model.Workflow
getPublic.
getQCREPORT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Gets the value of the qcreport property.
getQtype() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
Gets the value of the qtype property.
getQualityMultiplier() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field qualityMultiplier.
getQualityNumberOfLevels() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field qualityNumberOfLevels.
getQualityScorer() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field qualityScorer.
getQUALITYSCORER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
Gets the value of the qualityscorer property.
getQUALITYSCORES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING
Gets the value of the qualityscores property.
getQualityType() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field qualityType.
getQuery(FeatureSet, int) - Method in interface com.github.seqware.queryengine.system.exporters.QueryDumperInterface
Return each of the getNumQueries
getQueryInterface() - Static method in class com.github.seqware.queryengine.factory.SWQEFactory
Get a reference to the currently operating Query Interface
getQueryValue(String) - Method in class net.sourceforge.seqware.webservice.resources.BasicRestlet
 
getQueue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
getQueue() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getRandom() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getReadBases() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field readBases.
getReadClass() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Getter for the field readClass.
getREADCLASS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Gets the value of the readclass property.
getReadCount() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field readCount.
getReader() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
Getter for the field reader.
getReadIndex() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Getter for the field readIndex.
getREADINDEX() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Gets the value of the readindex property.
getReadLabel() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Getter for the field readLabel.
getReadSpec() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
Getter for the field readSpec.
getREADSPEC() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
Gets the value of the readspec property.
getReadSpecs() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
Getter for the field readSpecs.
getReadsPerSpot() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
Getter for the field readsPerSpot.
getReadsSupportingCallOne() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field readsSupportingCallOne.
getReadsSupportingCallThree() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field readsSupportingCallThree.
getReadsSupportingCallTwo() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field readsSupportingCallTwo.
getReadType() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Getter for the field readType.
getREADTYPE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Gets the value of the readtype property.
getReadyToProcess() - Method in class net.sourceforge.seqware.common.model.SequencerRun
getReadyToProcess.
getReadyToProcess() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field readyToProcess.
getReducerClass() - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
 
getReference() - Method in class com.github.seqware.queryengine.model.FeatureSet
Get the reference for this featureSet
getReference() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
Get the reference for this featureSet
getReference() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
Get the reference for this featureSet
getREFERENCEALIGNMENT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Gets the value of the referencealignment property.
getReferenceAveSeqQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field referenceAveSeqQuality.
getReferenceBase() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field referenceBase.
getReferenceCallQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field referenceCallQuality.
getReferenceID() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getReferenceID() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getReferenceID() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getReferenceID() - Method in class com.github.seqware.queryengine.model.FeatureSet
Get the referenceID for the associated reference
getReferenceID() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
Get the referenceID for the associated reference
getReferenceID() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
Get the referenceID for the associated reference
getReferenceId() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Getter for the field referenceId.
getReferenceIDBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getReferenceIDOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
getReferenceIDOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getReferenceIDOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
getReferenceIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getReferenceIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getReferenceIDs(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getReferenceIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getReferenceIDsBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getReferenceIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getReferenceIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getReferenceIDsCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getReferenceIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getReferenceIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getReferenceIDsList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getReferenceIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getReferenceIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getReferenceIDsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getReferenceIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
getReferenceIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getReferenceIDsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
getReferenceMaxSeqQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field referenceMaxSeqQuality.
getReferenceName() - Method in class com.github.seqware.queryengine.util.FSGID
Getter for the field referenceName.
getReferences() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd
getReferences.
getReferences() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
getReferences.
getReferences() - Method in interface com.github.seqware.queryengine.model.QueryInterface
getReferences.
getReferences(ReferenceSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
getReferences.
getReferenceSets() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd
getReferenceSets.
getReferenceSets() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
getReferenceSets.
getReferenceSets() - Method in interface com.github.seqware.queryengine.model.QueryInterface
getReferenceSets.
getReferenceSets() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
getReferenceSets.
getRefLane() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field refLane.
getRefLane() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field refLane.
getRefName() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getRefName() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getRefName() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF
Gets the value of the refname property.
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF
Gets the value of the refname property.
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF
Gets the value of the refname property.
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF
Gets the value of the refname property.
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR
Gets the value of the refname property.
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF
Gets the value of the refname property.
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF
Gets the value of the refname property.
getRegion() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Gets the value of the region property.
getRegions() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field regions.
getRegions() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field regions.
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
Getter for the field registration.
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareFile
Getter for the field registration.
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareLane
Getter for the field registration.
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
Getter for the field registration.
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareSample
Getter for the field registration.
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareStudy
Getter for the field registration.
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
Getter for the field registration.
getRegistration(HttpServletRequest) - Static method in class net.sourceforge.solexatools.Security
getRegistration.
getRegistrationId() - Method in class net.sourceforge.seqware.common.model.Registration
Getter for the field registrationId.
getRegistrationService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field registrationService.
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
Getter for the field registrationService.
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController
Getter for the field registrationService.
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.LoginController
Getter for the field registrationService.
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
Getter for the field registrationService.
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController
Getter for the field registrationService.
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
Getter for the field registrationService.
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.SignUpController
Getter for the field registrationService.
getRegistrationServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getRegistrationServiceBean.
getRelationship() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
Getter for the field relationship.
getRelativeLocation() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field relativeLocation.
getRELEASE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Gets the value of the release property.
getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.business.FileReportService
getReportForSequencerRun.
getReportForSequencerRun(SequencerRun, String, String) - Method in interface net.sourceforge.seqware.common.business.FileReportService
getReportForSequencerRun.
getReportForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.FileReportService
getReportForSequencerRun.
getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
getReportForSequencerRun.
getReportForSequencerRun(SequencerRun, String, String) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
getReportForSequencerRun.
getReportForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
getReportForSequencerRun.
getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
getReportForSequencerRun.
getReportForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
getReportForSequencerRun.
getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
getReportForSequencerRun.
getReportForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
getReportForSequencerRun.
getReportForSequencerRuns(String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
getReportForSequencerRuns.
getReportForSequencerRuns(String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
getReportForSequencerRuns.
getReportForStudy(Study) - Method in interface net.sourceforge.seqware.common.business.FileReportService
getReportForStudy.
getReportForStudy(Study, String, String, int, int) - Method in interface net.sourceforge.seqware.common.business.FileReportService
getReportForStudy.
getReportForStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
getReportForStudy.
getReportForStudy(Study, String, String, int, int) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
getReportForStudy.
getReportForStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
getReportForStudy.
getReportForStudy(Study, String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO
getReportForStudy.
getReportForStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
getReportForStudy.
getReportForStudy(Study, String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
getReportForStudy.
getRepresentation(Document) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools
getRepresentation.
getRequestedTypeList(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.ControllerUtil
getRequestedTypeList.
getRequestedTypeList(HttpServletRequest) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
getRequestedTypeList.
getRequirements() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
get job requirements
getResourceInfo(ApplicationInfo) - Method in class net.sourceforge.seqware.webservice.resources.queries.GenericDBResource
getResultClass() - Method in interface com.github.seqware.queryengine.plugins.PluginInterface
 
getResultClass() - Method in class com.github.seqware.queryengine.plugins.plugins.FeaturesByFilterPlugin
 
getResultClass() - Method in class com.github.seqware.queryengine.plugins.plugins.FeatureSetCountPlugin
 
getResultClass() - Method in class com.github.seqware.queryengine.plugins.plugins.VCFDumperPlugin
 
getResultMechanism() - Method in interface com.github.seqware.queryengine.plugins.PluginInterface
 
getResultMechanism() - Method in class com.github.seqware.queryengine.plugins.plugins.FeaturesByFilterPlugin
 
getResultMechanism() - Method in class com.github.seqware.queryengine.plugins.plugins.FeatureSetCountPlugin
 
getResultMechanism() - Method in class com.github.seqware.queryengine.plugins.plugins.VCFDumperPlugin
 
getReturnValue() - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException
Getter for the field returnValue.
getReturnValue() - Method in class net.sourceforge.seqware.common.module.ReturnValue
Getter for the field returnValue.
getReturnValues() - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Getter for the field returnValues.
getRights(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getRights(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getRights(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
 
getRightsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getRightsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getRightsCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
 
getRightsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getRightsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getRightsList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
 
getRootProcessing(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
getRootProcessing.
getRootProcessing(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
getRootProcessing.
getRootProcessing(WorkflowRun) - Static method in class net.sourceforge.solexatools.util.FindChildUtil
getRootProcessing.
getRootProcessingName() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getRootProcessingSwa() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getRootSample(Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
getRootSample.
getRootSample(Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService
getRootSample.
getRootSample(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
getRootSample.
getRootSample(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
getRootSample.
getRootSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
Getter for the field rootSample.
getRootSamples(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
getRootSamples.
getRootSamples(Study) - Method in interface net.sourceforge.seqware.common.business.SampleService
getRootSamples.
getRootSamples(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
getRootSamples.
getRootSamples(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
getRootSamples.
getRowId() - Method in class net.sourceforge.seqware.common.model.FileReportRow
Getter for the field rowId.
getRowId() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
Getter for the field rowId.
getRowKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getRowKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getRowKey() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
getRowKey() - Method in class com.github.seqware.queryengine.util.FSGID
Output the portion of the SGID that is used as a rowKey
getRowKey() - Method in class com.github.seqware.queryengine.util.SGID
Output the portion of the SGID that is used as a rowKey
getRows() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
Getter for the field rows.
getRowsForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
getRowsForSequencerRun.
getRowsForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
getRowsForSequencerRun.
getRowsForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
getRowsForSequencerRun.
getRowsForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
getRowsForSequencerRun.
getRowsWithSequencerRuns() - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
getRowsWithSequencerRuns.
getRowsWithSequencerRuns() - Method in interface net.sourceforge.seqware.common.business.SampleReportService
getRowsWithSequencerRuns.
getRowsWithSequencerRuns() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
getRowsWithSequencerRuns.
getRowsWithSequencerRuns() - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
getRowsWithSequencerRuns.
getRUN() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunSet
Gets the value of the run property.
getRUNATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES
Gets the value of the runattribute property.
getRUNATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the runattributes property.
getRunCenter() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field runCenter.
getRunCenter() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field runCenter.
getRunCenter() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the runCenter property.
getRunDate() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the runDate property.
getRunFile() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the runFile property.
getRUNLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS
Gets the value of the runlink property.
getRUNLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the runlinks property.
getRunName() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getRunName() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.Header
Get the value of runName
getRunningCount(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
getRunningCount.
getRunningCount(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
getRunningCount.
getRUNREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Gets the value of the runref property.
getRunsFromWorkflow(Integer) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
Using a workflow SWID, find all of the workflow runs, and report on each of the workflow runs the files, samples and processing events associated with each.
getRunStartTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field runStartTimestamp.
getRunStartTstmp() - Method in class net.sourceforge.seqware.common.module.ReturnValue
Getter for the field runStartTstmp.
getRunStopTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field runStopTimestamp.
getRunStopTstmp() - Method in class net.sourceforge.seqware.common.module.ReturnValue
Getter for the field runStopTstmp.
getRunSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getS3InputStream(String, int, long, String, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
getS3InputStream.
getS3InputStream(String, int, long) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
getS3InputStream.
getS3Url(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
getS3Url.
getS3Url(String, String, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
getS3Url.
getSample() - Method in class net.sourceforge.seqware.common.model.FileReportRow
Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.common.model.IUS
Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.common.model.SampleLink
Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.common.model.SampleSearch
Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.common.model.ShareSample
Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.common.model.UploadSequence
Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
getSAMPLE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleSet
Gets the value of the sample property.
getSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Getter for the field sample.
getSample_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Getter for the field sample_url.
getSAMPLEATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES
Gets the value of the sampleattribute property.
getSampleAttributeId() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
Getter for the field sampleAttributeId.
getSampleAttributes() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field sampleAttributes.
getSAMPLEATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Gets the value of the sampleattributes property.
getSampleCode() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field sampleCode.
getSAMPLEDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
Gets the value of the sampledescriptor property.
getSampleHierarchies() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchies
 
getSampleHtml(Sample, Registration, String, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
getSampleHtml.
getSampleHtml(Sample, Registration, Integer) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
getSampleHtml.
getSampleId() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field sampleId.
getSampleId() - Method in class net.sourceforge.seqware.common.model.UploadSequence
Getter for the field sampleId.
getSampleId() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
Gets the value of the sampleId property.
getSampleId() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy
 
getSampleId() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
Gets the value of the sampleId property.
getSampleId() - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto
Getter for the field sampleId.
getSAMPLELINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS
Gets the value of the samplelink property.
getSampleLinkId() - Method in class net.sourceforge.seqware.common.model.SampleLink
Getter for the field sampleLinkId.
getSampleLinks() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field sampleLinks.
getSAMPLELINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Gets the value of the samplelinks property.
getSampleName() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getSAMPLENAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Gets the value of the samplename property.
getSAMPLEPOOLREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Gets the value of the samplepoolref property.
getSAMPLEREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Gets the value of the sampleref property.
getSampleRef() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
Gets the value of the sampleRef property.
getSampleRef() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
Gets the value of the sampleRef property.
getSampleReportService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field sampleReportService.
getSampleReportServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getSampleReportServiceBean.
getSamples() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field samples.
getSamples() - Method in class net.sourceforge.seqware.common.model.Lane
getSamples.
getSamples() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field samples.
getSamples() - Method in class net.sourceforge.seqware.common.model.Project
Getter for the field samples.
getSamples() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field samples.
getSamples() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.RunInfo
 
getSampleSearch() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
Getter for the field sampleSearch.
getSampleSearchAttributeId() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
Getter for the field sampleSearchAttributeId.
getSampleSearchAttributes() - Method in class net.sourceforge.seqware.common.model.SampleSearch
Getter for the field sampleSearchAttributes.
getSampleSearchId() - Method in class net.sourceforge.seqware.common.model.SampleSearch
Getter for the field sampleSearchId.
getSampleSearchService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field sampleSearchService.
getSampleSearchServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getSampleSearchServiceBean.
getSampleService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.validation.SampleValidator
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
Getter for the field sampleService.
getSampleServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getSampleServiceBean.
getSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getSamplesFrom(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
Get the samples from an experiment.
getSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getSamplesFrom(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getSampleSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getSampleSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getSampleType() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field sampleType.
getSampleUrl() - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto
Getter for the field sampleUrl.
getSchema() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
Gets the value of the schema property.
getSchema() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
Gets the value of the schema property.
getScore() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getScore() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getScore() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getScore() - Method in class com.github.seqware.queryengine.model.Feature
(GVF: The score of the feature, an integer or floating point number.)
getScore() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Getter for the field score.
getSector() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Gets the value of the sector property.
getSelectedIds(HttpServletRequest, String, String[], String[]) - Static method in class net.sourceforge.solexatools.util.BulkUtil
getSelectedIds.
getSelectedWorkflowParamValue(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
getSelectedWorkflowParamValue.
getSelection() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Getter for the field selection.
getSender() - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
Getter for the field sender.
getSeqid() - Method in class com.github.seqware.queryengine.model.Feature
User provided ID for the feature (GVF: The chromosome or contig on which the sequence_alteration is located (text).)
getSequenceOntologyAccession(String) - Static method in class com.github.seqware.queryengine.kernel.Compression
getSequenceOntologyAccession.
getSequenceOntologyAccessionSurrogate(String) - Static method in class com.github.seqware.queryengine.kernel.Compression
Returns the compressed surrogate for a particular SO accession.
getSequencer_run_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Getter for the field sequencer_run_url.
getSequencerRun() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field sequencerRun.
getSequencerRun() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
Getter for the field sequencerRun.
getSequencerRun() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
Getter for the field sequencerRun.
getSequencerRun() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
Getter for the field sequencerRun.
getSequencerRun() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
getSequencerRun(Lane) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
getSequencerRun.
getSequencerRun(Processing) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
getSequencerRun.
getSequencerRun() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem
Getter for the field sequencerRun.
getSequencerRunAttributeId() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
Getter for the field sequencerRunAttributeId.
getSequencerRunAttributes() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field sequencerRunAttributes.
getSequencerRunHtml(SequencerRun, Registration, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
getSequencerRunHtml.
getSequencerRunId() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field sequencerRunId.
getSequencerRunId() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field sequencerRunId.
getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
getSequencerRunReport.
getSequencerRunReport() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getSequencerRunReport.
getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
getSequencerRunReport.
getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getSequencerRunReport.
getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
getSequencerRunReportIds.
getSequencerRunReportIds(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
getSequencerRunReportIds.
getSequencerRunReportIds(SequencerRun, String, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
getSequencerRunReportIds.
getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
getSequencerRunReportIds.
getSequencerRunReportIds(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
getSequencerRunReportIds.
getSequencerRunReportIds(SequencerRun, String, String) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
getSequencerRunReportIds.
getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
getSequencerRunReportIds.
getSequencerRunReportIds(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
getSequencerRunReportIds.
getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
getSequencerRunReportIds.
getSequencerRunReportIds(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
getSequencerRunReportIds.
getSequencerRuns() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field sequencerRuns.
getSequencerRunService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListController
Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController
Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO
Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
Getter for the field sequencerRunService.
getSequencerRunServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getSequencerRunServiceBean.
getSequencerRunSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getSequencerRunValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Getter for the field sequencerRunValidator.
getSequencerRunWizardDTO() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
getSequencerRunWizardDTO.
getSequencerRunWizardValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Getter for the field sequencerRunWizardValidator.
getSequenceSpace() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field sequenceSpace.
getSEQUENCESPACE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS
Gets the value of the sequencespace property.
getSEQUENCINGPROTOCOL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Gets the value of the sequencingprotocol property.
getSeqware_version() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getSeqwareAccession() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
getSeqwareRevision() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field seqwareRevision.
getSeqwareVersion() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field seqwareVersion.
getSerialization() - Static method in class com.github.seqware.queryengine.factory.SWQEFactory
Get a reference to the current operating serialization method
getSerializationConstant() - Method in interface com.github.seqware.queryengine.backInterfaces.SerializationInterface
Stored as the first four bytes of serialization so that serialization types can pre-emptively handle their own forward/backward compatibility.
getSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getSerializationConstant() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getSerializationConstant() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getSerializationConstant() - Method in class com.github.seqware.queryengine.impl.ApacheSerialization
Stored as the first four bytes of serialization so that serialization types can pre-emptively handle their own forward/backward compatibility.
getSerializationConstant() - Method in class com.github.seqware.queryengine.impl.KryoSerialization
Stored as the first four bytes of serialization so that serialization types can pre-emptively handle their own forward/backward compatibility.
getSerializationConstant() - Method in class com.github.seqware.queryengine.impl.ProtobufSerialization
Stored as the first four bytes of serialization so that serialization types can pre-emptively handle their own forward/backward compatibility.
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Lane
Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Platform
Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Processing
Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Project
Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Sample
Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Study
Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.StudyType
Getter for the field serialVersionUID.
getServer() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Getter for the field server.
getSessionFactory() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field sessionFactory.
getSessionFactoryBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getSessionFactoryBean.
getSettings() - Static method in class net.sourceforge.seqware.common.util.configtools.ConfigTools
 
getSettings(boolean) - Static method in class net.sourceforge.seqware.common.util.configtools.ConfigTools
The output keys are always uppercase!
getSettings() - Method in class net.sourceforge.seqware.queryengine.backend.factory.Factory
Getter for the field settings.
getSettings() - Method in interface net.sourceforge.seqware.queryengine.backend.factory.FactoryInterface
getSettings.
getSettings() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
getSettings.
getSettings() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
Getter for the field settings.
getSettings() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
Getter for the field settings.
getSettings() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
getSettings.
getSETTINGS_MAP() - Static method in class com.github.seqware.queryengine.Constants
Get the settings map.
getSettingsFilePath() - Static method in class net.sourceforge.seqware.common.util.configtools.ConfigTools
 
getSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getSgid() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getSgid() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getSgid() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
getSGID() - Method in interface com.github.seqware.queryengine.model.Atom
Get the universally unique identifier of this object.
getSGID() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Get the universally unique identifier of this object.
getSGID() - Method in class com.github.seqware.queryengine.util.LazyReference
Get the underlying SGID for the lazy reference
getSgidBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getSgidBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getSgidBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getSgidOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getSgidOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getSgidOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getSgidOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getSgidOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getSgidOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getSgidOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getSgidOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getSgidOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
getSharedStudies() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field sharedStudies.
getSharedWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field sharedWorkflowRuns.
getShareExperimentId() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
Getter for the field shareExperimentId.
getShareFileId() - Method in class net.sourceforge.seqware.common.model.ShareFile
Getter for the field shareFileId.
getShareLaneId() - Method in class net.sourceforge.seqware.common.model.ShareLane
Getter for the field shareLaneId.
getShareProcessingId() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
Getter for the field shareProcessingId.
getShareSampleId() - Method in class net.sourceforge.seqware.common.model.ShareSample
Getter for the field shareSampleId.
getShareStudyId() - Method in class net.sourceforge.seqware.common.model.ShareStudy
Getter for the field shareStudyId.
getShareStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
Getter for the field shareStudyService.
getShareStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Getter for the field shareStudyService.
getShareWorkflowRun(String, WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
getShareWorkflowRun.
getShareWorkflowRun(String, WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
getShareWorkflowRun.
getShareWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
Getter for the field shareWorkflowRunId.
getShareWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
Getter for the field shareWorkflowRunService.
getShareWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
Getter for the field shareWorkflowRunService.
getSINGLE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
Gets the value of the single property.
getSingleWorkflowRun(Integer) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
Using a workflow run SWID, report on the files, samples and processing events associated with the run.
getSite() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn
Getter for the field site.
getSize() - Method in class net.sourceforge.seqware.common.model.File
Getter for the field size.
getSize() - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
getSize() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
getSize() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
Getter for the field size.
getSkip() - Method in class net.sourceforge.seqware.common.model.IUS
Getter for the field skip.
getSkip() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field skip.
getSkip() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field skip.
getSkip() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field skip.
getSkip() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Getter for the field skip.
getSkipTxt() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field skipTxt.
getSlideOneFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field slideOneFilePath.
getSlideOneFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field slideOneFilePath.
getSlideOneLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field slideOneLaneCount.
getSlideOneLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field slideOneLaneCount.
getSlideTwoFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field slideTwoFilePath.
getSlideTwoFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field slideTwoFilePath.
getSlideTwoLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field slideTwoLaneCount.
getSlideTwoLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field slideTwoLaneCount.
getSortKeySample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Getter for the field sortKeySample.
getSource() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getSource() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getSource() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getSource() - Method in class com.github.seqware.queryengine.model.Feature
(GVF: The source is a free text qualifier intended to describe the algorithm or operating procedure that generated this feature.)
getSource() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Getter for the field source.
getSource() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Getter for the field source.
getSource() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
Gets the value of the source property.
getSource() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
Gets the value of the source property.
getSource() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
Gets the value of the source property.
getSourcePath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
 
getSourceReader(String, int, long) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
This attempts to resume if passed in startPosition > 0.
getSourceSet() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner.PluginRunnerMapper
 
getSourceSet() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryPluginRunner
 
getSourceSet() - Method in interface com.github.seqware.queryengine.plugins.MapperInterface
 
getSPOTDECODEMETHOD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR
Gets the value of the spotdecodemethod property.
getSPOTDECODESPEC() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR
Gets the value of the spotdecodespec property.
getSPOTDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
Gets the value of the spotdescriptor property.
getSpotDesignReadSpec() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field spotDesignReadSpec.
getSql() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
Getter for the field sql.
getStart() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getStart() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getStart() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getStart() - Method in class com.github.seqware.queryengine.model.Feature
Start coordinate, 0-based (GVF: 1-based integer for the beginning of the sequence_alteration locus on the plus strand (integer))
getStart() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
Getter for the field start.
getStartDate() - Method in class net.sourceforge.seqware.common.model.Invoice
Getter for the field startDate.
getStartPage() - Method in class net.sourceforge.solexatools.util.PageInfo
Getter for the field startPage.
getStartPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.ContigPosition
Getter for the field startPosition.
getStartPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
Getter for the field startPosition.
getStartPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field startPosition.
getState(Atom) - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Accessor method for the back-end.
getState() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager.AtomStatePair
 
getState(Atom) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Accessor method for the back-end.
getState() - Method in class net.sourceforge.seqware.common.model.Invoice
Getter for the field state.
getStats() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
Getter for the field stats.
getStatus(Study, Sample, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
getStatus.
getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
getStatus.
getStatus(Study, Sample, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
getStatus.
getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
getStatus.
getStatus(Study, Sample, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
getStatus.
getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
getStatus.
getStatus(Study, Sample, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
getStatus.
getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
getStatus.
getStatus() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field status.
getStatus() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field status.
getStatus() - Method in class net.sourceforge.seqware.common.model.Project
Getter for the field status.
getStatus() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
Getter for the field status.
getStatus() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field status.
getStatus() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field status.
getStatus() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field status.
getStatus() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field status.
getStatus() - Method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus
 
getStatus(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowEngine
find the workflow by input id, and return the status of the workflow
getStatus() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowEngine
 
getStatus(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine
 
getStatus() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine
 
getStatus(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.PegasusWorkflowEngine
 
getStatus() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.PegasusWorkflowEngine
 
getStatusCmd() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field statusCmd.
getStatusCount(Study, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
getStatusCount.
getStatusCount(Study, String) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
getStatusCount.
getStatusCounts() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
Getter for the field statusCounts.
getStatuses() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Getter for the field statuses.
getStatusesForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
getStatusesForSequencerRun.
getStatusesForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
getStatusesForSequencerRun.
getStatusesForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
getStatusesForSequencerRun.
getStatusesForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
getStatusesForSequencerRun.
getStatusesForStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
getStatusesForStudy.
getStatusesForStudy(Study) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
getStatusesForStudy.
getStatusesForStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
getStatusesForStudy.
getStatusesForStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
getStatusesForStudy.
getStatusesForWorkflow(Study, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
getStatusesForWorkflow.
getStatusesForWorkflow(SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
getStatusesForWorkflow.
getStatusesForWorkflow(Study, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
getStatusesForWorkflow.
getStatusesForWorkflow(SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
getStatusesForWorkflow.
getStatusesForWorkflow(Study, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
getStatusesForWorkflow.
getStatusesForWorkflow(SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
getStatusesForWorkflow.
getStatusesForWorkflow(Study, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
getStatusesForWorkflow.
getStatusesForWorkflow(SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
getStatusesForWorkflow.
getStderr() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field stderr.
getStdErr() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field stdErr.
getStderr() - Method in class net.sourceforge.seqware.common.module.ReturnValue
Getter for the field stderr.
getStdErr(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowEngine
find the workflow by input id, return the first failed job's error message if no failed job, return empty string
getStdErr(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine
 
getStdErr(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.PegasusWorkflowEngine
 
getStderrFile() - Method in class net.sourceforge.seqware.pipeline.module.Module
Getter for the file where the stderr will be redirected.
getStdout() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field stdout.
getStdOut() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field stdOut.
getStdout() - Method in class net.sourceforge.seqware.common.module.ReturnValue
Getter for the field stdout.
getStdOut(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowEngine
 
getStdOut(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine
 
getStdOut(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.PegasusWorkflowEngine
 
getStdoutFile() - Method in class net.sourceforge.seqware.pipeline.module.Module
Getter for the file where the stdout will be redirected.
getStop() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getStop() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getStop() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getStop() - Method in class com.github.seqware.queryengine.model.Feature
Stop coordinate, 0-based (GVF: 1-based integer of the end of the sequence_alteration on plus strand (integer).)
getStop() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
Getter for the field stop.
getStopPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.ContigPosition
Getter for the field stopPosition.
getStopPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
Getter for the field stopPosition.
getStopPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field stopPosition.
getStorage() - Static method in class com.github.seqware.queryengine.factory.SWQEFactory
Get a reference to the currently operating storage method
getStore(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.factory.Factory
getStore.
getStore(SeqWareSettings) - Method in interface net.sourceforge.seqware.queryengine.backend.factory.FactoryInterface
getStore.
getStore(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.factory.impl.BerkeleyDBFactory
getStore.
getStore() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Getter for the field store.
getStore() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
Getter for the field store.
getStore() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Getter for the field store.
getStore(String, Long, int) - Static method in class net.sourceforge.seqware.queryengine.webservice.model.BackendPool
getStore.
getStoreType() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Getter for the field storeType.
getStrand() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getStrand() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getStrand() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getStrand() - Method in class com.github.seqware.queryengine.model.Feature
Strand of the feature.
getStrand() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field strand.
getStrand() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Getter for the field strand.
getStrategy() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Getter for the field strategy.
getStrExpectedNumberReads() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field strExpectedNumberReads.
getStrExpectedNumberRuns() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field strExpectedNumberRuns.
getStrExpectedNumReads() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field strExpectedNumReads.
getStrExpectedNumRuns() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field strExpectedNumRuns.
getStrLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
Getter for the field strLaneCount.
getStrRefLane() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field strRefLane.
getStrStartURL() - Method in class net.sourceforge.seqware.common.business.UploadFile
Getter for the field strStartURL.
getStrStartURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
Getter for the field strStartURL.
getStudies() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field studies.
getStudy() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field study.
getStudy() - Method in class net.sourceforge.seqware.common.model.FileReportRow
Getter for the field study.
getStudy() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
Getter for the field study.
getStudy() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
Getter for the field study.
getStudy() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
Getter for the field study.
getStudy() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
Getter for the field study.
getStudy() - Method in class net.sourceforge.seqware.common.model.StudyLink
Getter for the field study.
getSTUDY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudySet
Gets the value of the study property.
getStudy(Experiment) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
getStudy.
getStudy(Sample) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
getStudy.
getStudy(Lane) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
getStudy.
getStudy(Processing) - Static method in class net.sourceforge.solexatools.util.FindRootUtil
getStudy.
getSTUDYABSTRACT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Gets the value of the studyabstract property.
getSTUDYATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES
Gets the value of the studyattribute property.
getStudyAttributeId() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
Getter for the field studyAttributeId.
getStudyAttributes() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field studyAttributes.
getSTUDYATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Gets the value of the studyattributes property.
getStudyDAO() - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
Getter for the field studyDAO.
getSTUDYDESCRIPTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Gets the value of the studydescription property.
getStudyId() - Method in class net.sourceforge.seqware.common.model.ShareStudy
Getter for the field studyId.
getStudyId() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field studyId.
getSTUDYLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS
Gets the value of the studylink property.
getStudyLinkId() - Method in class net.sourceforge.seqware.common.model.StudyLink
Getter for the field studyLinkId.
getStudyLinks() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field studyLinks.
getSTUDYLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Gets the value of the studylinks property.
getSTUDYREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Gets the value of the studyref property.
getSTUDYREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the studyref property.
getStudyService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.validation.StudyValidator
Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController
Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController
Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListController
Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportController
Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
Getter for the field studyService.
getStudyServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getStudyServiceBean.
getStudySwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
getStudyTitle() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.Header
Get the value of studyTitle
getSTUDYTITLE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Gets the value of the studytitle property.
getStudyType() - Method in class net.sourceforge.seqware.common.model.Lane
 
getSTUDYTYPE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Gets the value of the studytype property.
getStudyTypeDAO() - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
Getter for the field studyTypeDAO.
getStudyTypeId() - Method in class net.sourceforge.seqware.common.model.StudyType
Getter for the field studyTypeId.
getStudyTypes() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getStudyTypes() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getStudyTypes.
getStudyTypes() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getStudyTypes() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getStudyTypeService() - Method in class net.sourceforge.seqware.common.ContextImpl
 
getStudyTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Getter for the field studyTypeService.
getStudyTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
Getter for the field studyTypeService.
getStudyTypeServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getStudyTypeServiceBean.
getStydyHtml(Study, Registration, String, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
getStydyHtml.
getStydyHtml(Study, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
getStydyHtml.
getSubject(String, String, String) - Method in class net.sourceforge.solexatools.authentication.UNCKerberos
getSubject.
getSubjectEmail() - Method in class net.sourceforge.seqware.common.invitation.InvitationParams
Getter for the field subjectEmail.
getSUBMISSION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionSet
Gets the value of the submission property.
getSubmissionComment() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the submissionComment property.
getSubmissionDate() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the submissionDate property.
getSubmissionId() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the submissionId property.
getSum() - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage
Getter for the field sum.
getSummaryData(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
getSummaryData.
getSummaryLines() - Method in class net.sourceforge.solexatools.util.SummaryData
Getter for the field summaryLines.
getSUPPRESS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Gets the value of the suppress property.
getSvType() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field svType.
getSwa() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Getter for the field swa.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Expense
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.File
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Invoice
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.IUS
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareFile
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareLane
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareSample
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareStudy
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field swAccession.
getSwCluster() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
getSynonymMap() - Method in class com.github.seqware.queryengine.util.obo.OboParser
Hacked map of terms to synonyms
getSyntax(OptionParser, String) - Static method in class net.sourceforge.seqware.common.metadata.ProcessingTaskGroup.ProcessingTaskGroup
getSyntax.
getSyntax() - Static method in class net.sourceforge.seqware.pipeline.daxgenerator.Daxgenerator
getSyntax.
getSyntax(OptionParser, String) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner
getSyntax.
getTablename() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
getTablename.
getTablename() - Method in class com.github.seqware.queryengine.util.FSGID
getTablename.
getTag() - Method in interface net.sourceforge.seqware.common.model.Attribute
getTag.
getTag() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
Getter for the field tag.
getTag() - Method in class net.sourceforge.seqware.common.model.FileAttribute
getTag.
getTag() - Method in class net.sourceforge.seqware.common.model.IUS
Getter for the field tag.
getTag() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
getTag.
getTag() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
Getter for the field tag.
getTag() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
getTag.
getTag() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
getTag.
getTag() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
getTag.
getTag() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
Getter for the field tag.
getTag() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
getTag.
getTag() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
getTag.
getTag() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
getTag.
getTag() - Method in class net.sourceforge.seqware.queryengine.backend.model.Tag
Getter for the field tag.
getTag(Integer) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
getTag.
getTAG() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
Gets the value of the tag property.
getTAG() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
Gets the value of the tag property.
getTAG() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
Gets the value of the tag property.
getTAG() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
Gets the value of the tag property.
getTAG() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
Gets the value of the tag property.
getTagByKey(TagSet, String) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Quickly get the value of a tag by the key.
getTagByKey(String, String) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Quickly get the value of a tag by the key.
getTagByKey(String, String) - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable
Quickly get the value of a tag by the key.
getTagByKey(TagSet, String) - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable
Quickly get the value of a tag by the key.
getTagMetadata() - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
getTagMetadata.
getTagMetadata(long) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
getTagMetadata.
getTags(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getTags(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getTags(int) - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getTags(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getTags(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getTags(int) - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getTags() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd
getTags.
getTags() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
getTags.
getTags() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Get tags that the implementing class has been tagged with
getTags() - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable
Get tags that the implementing class has been tagged with
getTags() - Method in interface com.github.seqware.queryengine.model.QueryInterface
getTags.
getTags() - Method in class com.github.seqware.queryengine.model.Tag
Get tags that the implementing class has been tagged with
getTags() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field tags.
getTags() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field tags.
getTags() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
the key-value from metadata.xml
getTags() - Method in class net.sourceforge.seqware.queryengine.backend.model.Model
Getter for the field tags.
getTags() - Method in interface net.sourceforge.seqware.queryengine.backend.model.ModelInterface
getTags.
getTags() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field tags.
getTags(Integer) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
getTags.
getTags(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
getTags.
getTagsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getTagsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getTagsBuilderList() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getTagsBuilderList() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getTagsCount() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getTagsCount() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getTagsCount() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getTagsCount() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getTagsCount() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getTagsCount() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getTagSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getTagSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getTagSet() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getTagSet() - Method in class com.github.seqware.queryengine.model.Tag
Get a reference to the parent TagSet
getTagSetBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getTagSetIDs() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Getter for the field tagSetIDs.
getTagSetOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getTagSetOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getTagSetOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getTagSetRowKey() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagHierarchicalOccurrence
 
getTagSetRowKey() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagOccurrence
 
getTagSetRowKey() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagValue
 
getTagSetRowKey() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagValuePresence
 
getTagSets() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd
getTagSets.
getTagSets() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
getTagSets.
getTagSets() - Method in interface com.github.seqware.queryengine.model.QueryInterface
getTagSets.
getTagSets() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
getTagSets.
getTagSetSGID() - Method in class com.github.seqware.queryengine.model.Tag
Get a reference to the parent TagSet
getTagsList() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getTagsList() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getTagsList() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getTagsList() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getTagsList() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getTagsList() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getTagsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getTagsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getTagsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getTagsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getTagsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getTagsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getTagsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
getTagsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
getTagsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
getTagsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
getTagsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
getTagsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
getTagSpec(String) - Method in class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker
Given a key, locate a potential match inside a list of tag sets, otherwise create a new one in the ad hoc set.
getTagSpec() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
Getter for the field tagSpec.
getTagSpecIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getTagSpecIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getTagSpecIDs(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getTagSpecIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getTagSpecIDsBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getTagSpecIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getTagSpecIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getTagSpecIDsCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getTagSpecIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getTagSpecIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getTagSpecIDsList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getTagSpecIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getTagSpecIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getTagSpecIDsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getTagSpecIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
getTagSpecIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
getTagSpecIDsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
getTagValue(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
getTagValue.
getTagValue(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
getTagValue.
getTarget() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
Gets the value of the target property.
getTarget() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
Gets the value of the target property.
getTarget() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE
Gets the value of the target property.
getTarget() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS
Gets the value of the target property.
getTargetedResequencing() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Get the value of targetedResequencing
getTAXONID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
Gets the value of the taxonid property.
getTemplate() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field template.
getTemplate() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field template.
getTemplateEmail() - Method in class net.sourceforge.seqware.common.invitation.InvitationParams
Getter for the field templateEmail.
getTemplateFile() - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
Getter for the field templateFile.
getTemplatePath() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Getter for the field templatePath.
getTemplateType() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Get the value of templateType
getTemplateType() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
Getter for the field templateType.
getTerm_name() - Method in enum com.github.seqware.queryengine.Constants.Term
 
getTermValue(Class<T>) - Method in enum com.github.seqware.queryengine.Constants.Term
 
getTest() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
getTEST_FAMILY_INBYTES() - Static method in class com.github.seqware.queryengine.impl.HBaseStorage
getTEST_FAMILY_INBYTES.
getTestCmd() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Getter for the field testCmd.
getTests() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
getThickEnd() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Getter for the field thickEnd.
getThickStart() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Getter for the field thickStart.
getThreads() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
getThreads() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
 
getTimestamp() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
getTimestamp() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
getTimestamp() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
 
getTimestamp() - Method in interface com.github.seqware.queryengine.model.Atom
Get a creation time for this resource.
getTimestamp() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Get a creation time for this resource.
getTimeTaken() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
Getter for the field timeTaken.
gettIO() - Method in class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
Proto-buffer
getTissSource() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
Getter for the field tissSource.
getTissueOrigin() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Get the value of tissueOrigin
getTissuePreparation() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Get the value of tissuePreparation
getTissueRegion() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Get the value of tissueRegion
getTissueType() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Get the value of tissueType
getTitle() - Method in enum net.sourceforge.seqware.common.hibernate.FindAllTheFiles.Header
 
getTitle() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field title.
getTitle() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field title.
getTitle() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field title.
getTITLE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Gets the value of the title property.
getTITLE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Gets the value of the title property.
getTITLE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Gets the value of the title property.
getTokenNames() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Getter for the field tokenNames.
getTombstone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
getTombstone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
getTombstone() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
getTotal() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
Getter for the field total.
getTotalDataBlocks() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Gets the value of the totalDataBlocks property.
getTotalPrice() - Method in class net.sourceforge.seqware.common.model.Expense
Getter for the field totalPrice.
getTotalPriceString() - Method in class net.sourceforge.seqware.common.model.Expense
Getter for the field totalPrice.
getTotalReads() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Gets the value of the totalReads property.
getTotalSpots() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Gets the value of the totalSpots property.
getTotalUnits() - Method in class net.sourceforge.seqware.common.model.Expense
Getter for the field totalUnits.
getTRANSCRIPTASSEMBLY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Gets the value of the transcriptassembly property.
getTranscriptId() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Getter for the field transcriptId.
getTRANSCRIPTSEQUENCING() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Gets the value of the transcriptsequencing property.
getTranslatedSequence() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Getter for the field translatedSequence.
getTranslocationDestinationContig() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field translocationDestinationContig.
getTranslocationDestinationStartPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field translocationDestinationStartPosition.
getTranslocationDestinationStopPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field translocationDestinationStopPosition.
getTranslocationType() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field translocationType.
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.comment_return
 
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.comparison_return
 
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.constant_return
 
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.constraint_return
 
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.high_precedence_constraint_return
 
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.identifier_return
 
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.key_value_function_return
 
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.literal_return
 
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.low_precedence_constraint_return
 
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.nested_constraint_return
 
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.query_return
 
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.three_param_predicate_return
 
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.two_param_predicate_return
 
getTreeAdaptor() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
getTreeAdaptor.
getTTL() - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl
Return the expiry date in terms of hours in the future (may fail if the time difference is too large)
getTTL() - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable
Return the expiry date in terms of hours in the future (may fail if the time difference is too large)
getType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
getType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
getType() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
getType() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagValuePresence
 
getType() - Method in class com.github.seqware.queryengine.model.Feature
(From GVF: The type of the feature, this is constrained to be either: (a) the SO term sequence_alteration (SO:0001059), (b) a child term of sequence_alteration, (c) the SO term gap (SO:0000730), or (d) the SO accession number for any of the previous terms.)
getType() - Method in class net.sourceforge.seqware.common.model.File
Getter for the field type.
getType() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field type.
getType() - Method in class net.sourceforge.seqware.common.model.UploadSequence
Getter for the field type.
getType() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Getter for the field type.
getType() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
Getter for the field type.
getType() - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
getType() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
 
getType() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
 
getType() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field type.
getType() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
Getter for the field type.
getType() - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
Getter for the field type.
getTypeNode() - Method in class net.sourceforge.seqware.common.business.UploadFile
Getter for the field typeNode.
getUids(NamingEnumeration<SearchResult>) - Method in class net.sourceforge.solexatools.authentication.OICRLdapAuthentication
getUids.
getUniqueDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
return the unqiue dir associate with the file if the file type is input, the provisioned file will be output to provisionfiles/uniquedir + filename
getUniqueName() - Method in class com.github.seqware.queryengine.kernel.RPNStack.Parameter
 
getUniqueName() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagValuePresence
 
getUnit() - Method in interface net.sourceforge.seqware.common.model.Attribute
getUnit.
getUnit() - Method in class net.sourceforge.seqware.common.model.FileAttribute
getUnit.
getUnit() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
getUnit.
getUnit() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
getUnit.
getUnit() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
getUnit.
getUnit() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
getUnit.
getUnit() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
getUnit.
getUnit() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
getUnit.
getUnit() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
getUnit.
getUnit() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
getUnit.
getUnit() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
Getter for the field unit.
getUnits() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
Getter for the field units.
getUnits() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
Getter for the field units.
getUnits() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
Getter for the field units.
getUnits() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
Getter for the field units.
getUnits() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
Getter for the field units.
getUnits() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
Getter for the field units.
getUnits() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
Getter for the field units.
getUNITS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
Gets the value of the units property.
getUNITS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
Gets the value of the units property.
getUNITS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
Gets the value of the units property.
getUNITS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
Gets the value of the units property.
getUNITS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
Gets the value of the units property.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Experiment
Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.IUS
Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Project
Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Registration
Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Sample
Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareStudy
Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Study
Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field updateTimestamp.
getUpdateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Getter for the field updateTimeStamp.
getUpdateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Getter for the field updateTimeStamp.
getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareExperiment
Getter for the field updateTstmp.
getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareFile
Getter for the field updateTstmp.
getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareLane
Getter for the field updateTstmp.
getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareProcessing
Getter for the field updateTstmp.
getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareSample
Getter for the field updateTstmp.
getUpdateValidator() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Getter for the field updateValidator.
getUpdateValidator() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
getUpdateValidator.
getUrl() - Method in class net.sourceforge.seqware.common.model.ExperimentLink
Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.File
Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.IUSLink
Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.LaneLink
Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingIus
Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.SampleLink
Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.StudyLink
Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
getUrl() - Method in class net.sourceforge.seqware.common.module.ReturnValue
Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn
Getter for the field url.
getURL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
Gets the value of the url property.
getURL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
Gets the value of the url property.
getURL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK
Gets the value of the url property.
getURL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
Gets the value of the url property.
getURL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK
Gets the value of the url property.
getUrl() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.webservice.dto.FileDto
Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto
Getter for the field url.
getUrlLabel() - Method in class net.sourceforge.seqware.common.model.File
Getter for the field urlLabel.
getUrlLabel() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field urlLabel.
getUrlLabel() - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
getUrlLabel() - Method in class net.sourceforge.seqware.common.module.ReturnValue
Getter for the field urlLabel.
getURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
Gets the value of the urllink property.
getURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
Gets the value of the urllink property.
getURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK
Gets the value of the urllink property.
getURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK
Gets the value of the urllink property.
getURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK
Gets the value of the urllink property.
getUrlString() - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
Getter for the field urlString.
getUseIparIntensities() - Method in class net.sourceforge.seqware.common.model.SequencerRun
Getter for the field useIparIntensities.
getUseIparIntensities() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Getter for the field useIparIntensities.
getUseOneURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
Getter for the field useOneURL.
getUser() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getUser() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getUser() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
 
getUserBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getUsername() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field username.
getUserName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field userName.
getUsername() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Getter for the field username.
getUserOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
getUserOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
getUserOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
 
getUsers(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getUsers(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getUsers(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getUsers() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd
Gets all users in all groups
getUsers() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
Gets all users in all groups
getUsers() - Method in interface com.github.seqware.queryengine.model.QueryInterface
Gets all users in all groups
getUsers() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
getUsers.
getUsersBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getUsersBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getUsersCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getUsersCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getUsersCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getUsersList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getUsersList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getUsersList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getUsersOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getUsersOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getUsersOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getUsersOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
getUsersOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
getUsersOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
getUseTwoURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence
Getter for the field useTwoURL.
getUseURL() - Method in class net.sourceforge.seqware.common.business.UploadFile
Getter for the field useURL.
getUuid() - Method in class com.github.seqware.queryengine.util.SGID
Get underlying UUID implementation, should only be called within the back-end
getVALIDATE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Gets the value of the validate property.
getValidationReportService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field validationReportService.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.FileController
Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
getValidator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
Getter for the field validator.
getValue() - Method in class com.github.seqware.queryengine.kernel.RPNStack.Constant
 
getValue() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagValuePresence
 
getValue() - Method in class com.github.seqware.queryengine.model.Tag
Get the value.
getValue() - Method in interface net.sourceforge.seqware.common.model.Attribute
getValue.
getValue() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
Getter for the field value.
getValue() - Method in class net.sourceforge.seqware.common.model.FileAttribute
getValue.
getValue() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
getValue.
getValue() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
Getter for the field value.
getValue() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
getValue.
getValue() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
getValue.
getValue() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
getValue.
getValue() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
Getter for the field value.
getValue() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
getValue.
getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
getValue.
getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Getter for the field value.
getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
Getter for the field value.
getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
getValue.
getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
Getter for the field value.
getValue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
Getter for the field value.
getValue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
Getter for the field value.
getValue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
 
getValue() - Method in class net.sourceforge.seqware.queryengine.backend.model.Tag
Getter for the field value.
getVALUE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
Gets the value of the value property.
getVALUE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
Gets the value of the value property.
getValue() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
Gets the value of the value property.
getVALUE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
Gets the value of the value property.
getVALUE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
Gets the value of the value property.
getVALUE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
Gets the value of the value property.
getValue() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
Getter for the field value.
getValueDescriptor() - Method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
getValues() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Getter for the field values.
getVBytes() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getVBytes() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getVBytes() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getVCFFeatureListing(String) - Method in class com.github.seqware.queryengine.system.rest.resources.FeatureSetResource
Return the features that belong to the specified feature set in VCF
getVDouble() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getVDouble() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getVDouble() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getVersion() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
getVersion.
getVersion() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Get version for the subject
getVersion() - Method in interface com.github.seqware.queryengine.model.interfaces.Versionable
Get version for the subject
getVersion() - Method in interface com.github.seqware.queryengine.model.QueryInterface
getVersion.
getVersion() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field version.
getVersion() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field version.
getVersion() - Method in class net.sourceforge.seqware.common.module.ReturnValue
Getter for the field version.
getVersion() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Getter for the field version.
getVersion() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getVersion() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
 
getVersion() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
getVersion.
getVFloat() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getVFloat() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getVFloat() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getViewName(String) - Static method in class net.sourceforge.solexatools.util.Constant
getViewName.
getVInteger() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getVInteger() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getVInteger() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getVisibleParams() - Method in class net.sourceforge.solexatools.util.SummaryData
Getter for the field visibleParams.
getVisibleWorkflowParams() - Method in class net.sourceforge.seqware.common.model.Workflow
getVisibleWorkflowParams.
getVisibleWorkflowParamsWithDifferentValue() - Method in class net.sourceforge.seqware.common.model.Workflow
getVisibleWorkflowParamsWithDifferentValue.
getVLong() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getVLong() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getVLong() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getVSGIDRef() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getVSGIDRef() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getVSGIDRef() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getVSGIDRefBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getVSGIDRefOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getVSGIDRefOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getVSGIDRefOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getVString() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
getVString() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
getVString() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
getvType() - Method in class com.github.seqware.queryengine.model.Tag
Get the type of value for the tag value
getWfRuns() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Getter for the field wfRuns.
getWidth() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
getWorkerName() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Getter for the field workerName.
getWorkerName() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Getter for the field workerName.
getWorkflow(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getWorkflow(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
Get a workflow
getWorkflow(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getWorkflow(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
Get a workflow
getWorkflow() - Method in class net.sourceforge.seqware.common.model.SampleReportRow
Getter for the field workflow.
getWorkflow() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
Getter for the field workflow.
getWorkflow() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Getter for the field workflow.
getWorkflow() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field workflow.
getWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getWorkflow_accession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getWorkflow_directory_name() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getWorkflow_engine() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getWorkflow_run_accession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
getWorkflowAccession.
getWorkflowAccession(String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getWorkflowAccession.
getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
getWorkflowAccession.
getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getWorkflowAccession.
getWorkflowAccession() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getWorkflowAccession() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Getter for the field workflowAccession.
getWorkflowAccession() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
getWorkflowAccession(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
getWorkflowAccession.
getWorkflowAccessionsToCheck() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
getWorkflowAttributeId() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
Getter for the field workflowAttributeId.
getWorkflowAttributes() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field workflowAttributes.
getWorkflowBaseDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getWorkflowBundleDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
getWorkflowBundleDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
getWorkflowClass() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getWorkflowClass() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getWorkflowDataModel(Integer, Integer) - Method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowDataModelFactory
load metadata.xml, if FTL, parse the FTL to XML, and translate it to Java based Object if Java, load the class.
getWorkflowDir() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Getter for the field workflowDir.
getWorkflowEngine() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getWorkflowEngine() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
getWorkflowEngine() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getWorkflowEngine(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
 
getWorkflowId() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field workflowId.
getWorkflowInfo() - Method in class net.sourceforge.seqware.pipeline.bundle.BundleInfo
getWorkflowInfo.
getWorkflowMetadata() - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
getWorkflowMetadata.
getWorkflowParam() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
Getter for the field workflowParam.
getWorkflowParamId() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Getter for the field workflowParamId.
getWorkflowParamId() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
Getter for the field workflowParamId.
getWorkflowParamMetadata(Integer) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
getWorkflowParamMetadata.
getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
getWorkflowParams.
getWorkflowParams(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getWorkflowParams.
getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
getWorkflowParams.
getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getWorkflowParams.
getWorkflowParams() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field workflowParams.
getWorkflowParamService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field workflowParamService.
getWorkflowParamService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
Getter for the field workflowParamService.
getWorkflowParamService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController
Getter for the field workflowParamService.
getWorkflowParamService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
Getter for the field workflowParamService.
getWorkflowParamServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getWorkflowParamServiceBean.
getWorkflowParamsWithDifferentFileMetaType() - Method in class net.sourceforge.seqware.common.model.Workflow
getWorkflowParamsWithDifferentFileMetaType.
getWorkflowParamValueId() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
Getter for the field workflowParamValueId.
getWorkflowParamValueService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field workflowParamValueService.
getWorkflowParamValueService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
Getter for the field workflowParamValueService.
getWorkflowParamValueService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
Getter for the field workflowParamValueService.
getWorkflowParamValueServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getWorkflowParamValueServiceBean.
getWorkflowRun() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
Getter for the field workflowRun.
getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
getWorkflowRun.
getWorkflowRun(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getWorkflowRun.
getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
getWorkflowRun.
getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getWorkflowRun.
getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.Expense
Getter for the field workflowRun.
getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field workflowRun.
getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
Getter for the field workflowRun.
getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
Getter for the field workflowRun.
getWorkflowRunAccession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
getWorkflowRunAccession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
getWorkflowRunAttributeId() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
Getter for the field workflowRunAttributeId.
getWorkflowRunAttributes() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field workflowRunAttributes.
getWorkflowRunByAncestorWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field workflowRunByAncestorWorkflowRunId.
getWorkflowRunHtml(WorkflowRun, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
getWorkflowRunHtml.
getWorkflowRunHtmlWithIUSs(WorkflowRun, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
getWorkflowRunHtmlWithIUSs.
getWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.Processing
Getter for the field workflowRunId.
getWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
Getter for the field workflowRunId.
getWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field workflowRunId.
getWorkflowRunInfo(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
getWorkflowRunInfo.
getWorkflowRunParam(SortedSet<WorkflowParam>) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
getWorkflowRunParam.
getWorkflowRunParamId() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
getWorkflowRunParamId.
getWorkflowRunParams() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Getter for the field workflowRunParams.
getWorkflowRunProcessings() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
Getter for the field workflowRunProcessings.
getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
getWorkflowRunReport.
getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
getWorkflowRunReport.
getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
getWorkflowRunReport.
getWorkflowRunReport(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getWorkflowRunReport.
getWorkflowRunReport(int, Date, Date) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getWorkflowRunReport.
getWorkflowRunReport(Date, Date) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getWorkflowRunReport.
getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
getWorkflowRunReport.
getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
getWorkflowRunReport.
getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
getWorkflowRunReport.
getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getWorkflowRunReport.
getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getWorkflowRunReport.
getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getWorkflowRunReport.
getWorkflowRunReportStdErr(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getWorkflowRunReportStdErr(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getWorkflowRunReportStdErr.
getWorkflowRunReportStdErr(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getWorkflowRunReportStdErr(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getWorkflowRunReportStdErr.
getWorkflowRunReportStdOut(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getWorkflowRunReportStdOut(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getWorkflowRunReportStdOut.
getWorkflowRunReportStdOut(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getWorkflowRunReportStdOut(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getWorkflowRunReportStdOut.
getWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.IUS
Getter for the field workflowRuns.
getWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.Lane
Getter for the field workflowRuns.
getWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.Workflow
Getter for the field workflowRuns.
getWorkflowRunsAssociatedWithFiles(List<Integer>, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
 
getWorkflowRunsAssociatedWithFiles(List<Integer>, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
Returns the workflow_runs associated with a group of files.
getWorkflowRunsAssociatedWithFiles(List<Integer>, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
getWorkflowRunsAssociatedWithFiles(List<Integer>, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
 
getWorkflowRunsByHost(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
getWorkflowRunsByHost.
getWorkflowRunsByHost(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getWorkflowRunsByHost.
getWorkflowRunsByHost(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
getWorkflowRunsByHost.
getWorkflowRunsByHost(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getWorkflowRunsByHost.
getWorkflowRunsByStatus(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
getWorkflowRunsByStatus.
getWorkflowRunsByStatus(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getWorkflowRunsByStatus.
getWorkflowRunsByStatus(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
getWorkflowRunsByStatus.
getWorkflowRunsByStatus(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getWorkflowRunsByStatus.
getWorkflowRunService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController
Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController
Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails
Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController
Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController
Getter for the field workflowRunService.
getWorkflowRunServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getWorkflowRunServiceBean.
getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
getWorkflowRunWithWorkflow.
getWorkflowRunWithWorkflow(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
getWorkflowRunWithWorkflow.
getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
getWorkflowRunWithWorkflow.
getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getWorkflowRunWithWorkflow.
getWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
getWorkflows.
getWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
getWorkflows.
getWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
getWorkflows.
getWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
getWorkflows.
getWorkflowsAndRuns() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
getWorkflowService() - Method in class net.sourceforge.seqware.common.ContextImpl
Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController
Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails
Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController
Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController
Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController
Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController
Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController
Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController
Getter for the field workflowService.
getWorkflowServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory
getWorkflowServiceBean.
getWorkflowsForStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
getWorkflowsForStudy.
getWorkflowsForStudy(Study) - Method in interface net.sourceforge.seqware.common.business.SampleReportService
getWorkflowsForStudy.
getWorkflowsForStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
getWorkflowsForStudy.
getWorkflowsForStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO
getWorkflowsForStudy.
getWorkflowSqwVersion() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
getWorkflowSqwVersion.
getWorkflowsRun() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
getWorkflowsRun.
getWorkflowState(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
This method examines a Pegasus log directory using the status command provided and will encode the state of the workflow in the ReturnValue object, running as ReturnValue.PROCESSING, failed as ReturnValue.FAILURE, and success as ReturnValue.SUCCESS.
getWorkflowType() - Method in class net.sourceforge.seqware.common.model.Workflow
 
getWorkflowType() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.ExperimentIDFilter
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.IUSIDFilter
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.LaneIDFilter
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.SampleIDFilter
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.StudyIDFilter
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentIDResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileIDResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusIDResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneIDResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrarySelectionResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrarySourceResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibraryStrategyResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.OrganismResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.PlatformResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessIDResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.RootSampleResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleIDResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunIDResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyIDResource
getXml.
getXML() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource
getXML.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyTypeResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource
getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource
getXml.
getXREFLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
Gets the value of the xreflink property.
getZygosity() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Getter for the field zygosity.
GFF3_DELETION - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GFF3_DELETION="deletion"
GFF3_INSERTION - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GFF3_INSERTION="insertion"
GFF3_SNV - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GFF3_SNV="VCF_SNV"
GFF3_UNKNOWN_TYPE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GFF3_UNKNOWN_TYPE="unknown_type"
GFF3VariantImportWorker - Class in com.github.seqware.queryengine.system.importers.workers
Ported GFF3VariantImportWorker now using our Hibernate-like entry.
GFF3VariantImportWorker() - Constructor for class com.github.seqware.queryengine.system.importers.workers.GFF3VariantImportWorker
Constructor for GFF3VariantImportWorker.
GFF3VariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
GFF3VariantImportWorker class.
GFF3VariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.GFF3VariantImportWorker
Constructor for GFF3VariantImportWorker.
GITest - Class in com.github.seqware.queryengine.tutorial
This is a quick and sample application built on top of our API, created for Poster testing.
GITest(String[]) - Constructor for class com.github.seqware.queryengine.tutorial.GITest
Constructor for GITest.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Expense
givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Experiment
givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.File
givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Invoice
givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.IUS
givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Lane
givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Processing
givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Registration
givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Sample
givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRun
givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Study
givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Workflow
givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
givesPermission.
givesPermission(Registration) - Method in interface net.sourceforge.seqware.common.security.PermissionsAware
givesPermission.
grabFeatureListsGivenRow(Result, SGID, SerializationInterface) - Static method in class com.github.seqware.queryengine.impl.HBaseStorage
grabFeatureListsGivenRow.
grabObjectsToBeFlushed() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
grabObjectsToBeFlushed.
gridProxyInit() - Static method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
Group - Interface in com.github.seqware.queryengine.model
A Group of users that may share ACL permissions
group - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
Group.Builder - Class in com.github.seqware.queryengine.model
 
Group.Builder() - Constructor for class com.github.seqware.queryengine.model.Group.Builder
 
GroupIO - Class in com.github.seqware.queryengine.impl.protobufIO
GroupIO class.
GroupIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.GroupIO
 
GroupListingResource - Class in com.github.seqware.queryengine.system.rest.resources
 
GroupListingResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.GroupListingResource
 
GroupResource - Class in com.github.seqware.queryengine.system.rest.resources
Group resource.
GroupResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.GroupResource
 
GRP_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
GRPS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
GT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant GT=11
GT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant GT=11
GTEQ - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant GTEQ=12
GTEQ - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant GTEQ=12
GVF_ALIAS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_ALIAS="Alias"
GVF_BREAKPOINT_DETAIL - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_BREAKPOINT_DETAIL="Breakpoint_detail"
GVF_DBXREF - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_DBXREF="Dbxref"
GVF_END_RANGE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_END_RANGE="End_range"
GVF_GENOTYPE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_GENOTYPE="Genotype"
GVF_HEMIZYGOUS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_HEMIZYGOUS="hemizygous"
GVF_HETEROZYGOUS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_HETEROZYGOUS="heterozygous"
GVF_HOMOZYGOUS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_HOMOZYGOUS="homozygous"
GVF_INDIVIDUAL - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_INDIVIDUAL="Individual"
GVF_PHASED - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_PHASED="Phased"
GVF_REFERENCE_AA - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_REFERENCE_AA="Reference_aa"
GVF_REFERENCE_CODON - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_REFERENCE_CODON="Reference_codon"
GVF_REFERENCE_SEQ - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_REFERENCE_SEQ="Reference_seq"
GVF_SEQUENCE_CONTEXT - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_SEQUENCE_CONTEXT="Sequence_context"
GVF_START_RANGE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_START_RANGE="Start_range"
GVF_TOTAL_READS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_TOTAL_READS="Total_reads"
GVF_VARIANT_AA - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_VARIANT_AA="Variant_aa"
GVF_VARIANT_CODON - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_VARIANT_CODON="Variant_codon"
GVF_VARIANT_EFFECT - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_VARIANT_EFFECT="Variant_effect"
GVF_VARIANT_FREQ - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_VARIANT_FREQ="Variant_freq"
GVF_VARIANT_READS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_VARIANT_READS="Variant_reads"
GVF_VARIANT_SEQ - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_VARIANT_SEQ="Variant_seq"
GVF_ZYGOSITY - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant GVF_ZYGOSITY="Zygosity"

H

HackedPosixParser - Class in org.apache.commons.cli
Workaround for bug with Apache CLI https://issues.apache.org/jira/browse/CLI-185 This can be removed when CLI 1.3 is released
HackedPosixParser() - Constructor for class org.apache.commons.cli.HackedPosixParser
 
handle(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication.OptionalSlashRedirect
 
handle(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion.OptionalSlashRedirect
 
handle - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.CycleCheckResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.GenericDBResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.ProcessIdProcessResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.RunWorkflowResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.SampleHierarchyResource
 
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.SampleIdFilesResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.SequencerRunIdFilesResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.SequencerRunReportResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesTSVResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowReportResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIdFilesResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDProcessingsResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDWorkflowResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRuntimeResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessingStructureResource
 
handle(Callback[]) - Method in class net.sourceforge.solexatools.authentication.UNCKerberos.NamePasswordCallbackHandler
 
handleAtom2PB(QESupporting.AtomPB, AtomImpl) - Static method in class com.github.seqware.queryengine.impl.protobufIO.UtilIO
Handle serialization of the core atom
handleAtom2PB(QESupporting.FeatureAtomPB, Feature) - Static method in class com.github.seqware.queryengine.impl.protobufIO.UtilIO
Handle serialization of the core atom just for Features
handleCancel(HttpServletRequest, HttpServletResponse, WorkflowRun) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
Handles the user's request to delete their study.
handleCancel(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.FileController
Handles the user's request to cancel the lane or the lane update page.
handleCancel(HttpServletRequest, HttpServletResponse, IUS) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
Handles the user's request to cancel.
handleCancel(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
Handles the user's request to cancel the lane or the lane update page.
handleCancel(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
Handles the user's request to cancel the sequencerRun or the sequencerRun update page.
handleCancel(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
Handles the user's request to cancel the registration or the registration update page.
handleCancel(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
Handles the user's request to cancel the experiment or the experiment update page.
handleCancel(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
Handles the user's request to cancel the experiment or the experiment update page.
handleCancel(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Handles the user's request to cancel the registration or the registration update page.
handleCancel(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
Handles the user's request to cancel the registration or the registration update page.
handleCompressedInput(String) - Static method in class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker
handleCompressedInput.
handleDelete(HttpServletRequest, HttpServletResponse, WorkflowRun) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
Handles the user's request to delete their study.
handleDelete(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Handles the user's request to delete their experiment.
handleDelete(HttpServletRequest, HttpServletResponse, File) - Method in class net.sourceforge.solexatools.webapp.controller.FileController
Handles the user's request to delete their file.
handleDelete(HttpServletRequest, HttpServletResponse, IUS) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
Handles the user's request to delete their ius.
handleDelete(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
Handles the user's request to delete their lane.
handleDelete(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
Handles the user's request to delete their processing.
handleDelete(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
Handles the user's request to delete their sample.
handleDelete(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Handles the user's request to delete their study.
handleDelete(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Handles the user's request to delete their study.
handleDelete(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
Handles the user's request to delete their study.
handleDelete(HttpServletRequest, HttpServletResponse, WorkflowParam) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
Handles the user's request to delete their study.
handleDelete(HttpServletRequest, HttpServletResponse, WorkflowParamValue) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
Handles the user's request to delete their study.
handleDeserialization(byte[]) - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
handleDeserialization(byte[]) - Method in interface com.github.seqware.queryengine.plugins.PluginInterface
 
handleFileResult(Path) - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner
 
handleGroupByAttribute(String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
handleMol2PB(QueryEngine.MoleculePB, MoleculeImpl) - Static method in class com.github.seqware.queryengine.impl.protobufIO.UtilIO
This should handle serialization of molecule
handleNext(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
Handles the user's request to submit a new study.
handleNext(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
Handles the user's request to submit a new study.
handlePB2Atom(QESupporting.AtomPB, AtomImpl) - Static method in class com.github.seqware.queryengine.impl.protobufIO.UtilIO
Handle de-serialization of the core atom
handlePB2Atom(QESupporting.FeatureAtomPB, Feature) - Static method in class com.github.seqware.queryengine.impl.protobufIO.UtilIO
Handle de-serialization of the core atom just for Features FIXME: this should be collapsible with normal atom
handlePB2Mol(QueryEngine.MoleculePB, MoleculeImpl) - Static method in class com.github.seqware.queryengine.impl.protobufIO.UtilIO
This should handle de-serialization of molecule
handlePrevious(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
Handles the user's request to cancel the study or the study update page.
handlePrevious(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
Handles the user's request to cancel the study or the study update page.
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AbortLoadIndexPageController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderSizeValidatorController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.CancelBulkDownloaderController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.CancelInputDownloaderController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ChangeNumberPopupPageController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.DeleteLoadedIndexPageController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.DownloaderController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.FileSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.IUSSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LogoutController
Handles a user's logout request.
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SignUpController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController
handleReset(HttpServletRequest, HttpServletResponse, Experiment) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Handles the user's request to reset the experiment page during a new or update experiment.
handleReset(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.FileController
Handles the user's request to reset the lane page during a new or update lane.
handleReset(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
Handles the user's request to reset the lane page during a new or update lane.
handleReset(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
Handles the user's request to reset the sequencerRun page during a new or update sequencerRun.
handleReset(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
Handles the user's request to reset the registration page during a new or update registration.
handleReset(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
Handles the user's request to reset the sample page during a new or update sample.
handleReset(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
Handles the user's request to reset the experiment page during a new or update experiment.
handleReset(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
Handles the user's request to reset the experiment page during a new or update experiment.
handleReset(HttpServletRequest, HttpServletResponse, SequencerRunWizardDTO) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Handles the user's request to reset the registration page during a new or update registration.
handleReset(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Handles the user's request to reset the study page during a new or update study.
handleReset(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
Handles the user's request to reset the study page during a new or update study.
handleReset(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
Handles the user's request to reset the study page during a new or update study.
handleReset(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
Handles the user's request to reset the study page during a new or update study.
handleReset(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
Handles the user's request to reset the registration page during a new or update registration.
handleSerialization(Object...) - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
handleSerialization(Object...) - Method in interface com.github.seqware.queryengine.plugins.PluginInterface
 
handleSerialization(Object...) - Method in class com.github.seqware.queryengine.plugins.plugins.FeatureSetCountPlugin
handleShare(HttpServletRequest, HttpServletResponse, WorkflowRun) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
Handles the user's request to share their WorkflowRun.
handleShare(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Handles the user's request to share their study.
handleShare(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
Handles the user's request to share their study.
handleSubmit(HttpServletRequest, HttpServletResponse, Experiment) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.FileController
Handles the user's request to submit a new lane.
handleSubmit(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
Handles the user's request to submit a new lane.
handleSubmit(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
Handles the user's request to submit a new sequencerRun.
handleSubmit(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
Handles the user's request to submit a new registration.
handleSubmit(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
Handles the user's request to submit a new experiment.
handleSubmit(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
Handles the user's request to submit a new experiment.
handleSubmit(HttpServletRequest, HttpServletResponse, SequencerRunWizardDTO) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Handles the user's request to submit a new registration.
handleSubmit(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, UploadFile) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, UploadSequence) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, WorkflowParam) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, WorkflowParamValue) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, SequencerRunWizardDTO) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
Handles the user's request to submit a new registration.
handleUpdate(HttpServletRequest, HttpServletResponse, Experiment) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Handles the user's request to update their study.
handleUpdate(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.FileController
Handles the user's request to update their lane.
handleUpdate(HttpServletRequest, HttpServletResponse, IUS) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
Handles the user's request to delete their ius.
handleUpdate(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
Handles the user's request to update their lane.
handleUpdate(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
Handles the user's request to update their sequencerRun.
handleUpdate(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
Handles the user's request to update their registration.
handleUpdate(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
Handles the user's request to update their study.
handleUpdate(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
Handles the user's request to update their experiment.
handleUpdate(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
Handles the user's request to update their experiment.
handleUpdate(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Handles the user's request to update their registration.
handleUpdate(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Handles the user's request to update their study.
handleUpdate(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
Handles the user's request to update their study.
handleUpdate(HttpServletRequest, HttpServletResponse, WorkflowParam) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
Handles the user's request to update their study.
handleUpdate(HttpServletRequest, HttpServletResponse, WorkflowParamValue) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
Handles the user's request to update their study.
handleUpdate(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
Handles the user's request to update their registration.
handleWorkflowRunsViaChild(Set<File>, Hibernate3DtoCopier) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource
 
handleWorkflowRunsViaIUS(Set<File>, Hibernate3DtoCopier) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource
 
handleWorkflowRunsViaLane(Set<File>, Hibernate3DtoCopier) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource
 
hasAcl() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
hasAcl() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
hasAcl() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginPBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginRunPBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
hasCascade() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
hasCascade() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
hasCascade() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
 
hasDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
hasDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
hasDate() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
hasDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
hasDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
hasDate() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
hasDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
hasDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
hasDescription() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
hasDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
hasDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
hasDescription() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
hasDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
hasDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
hasDescription() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginPBOrBuilder
 
hasEmailAddress() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
hasEmailAddress() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
hasEmailAddress() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
hasEmailAddressBeenUsed(String) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
hasEmailAddressBeenUsed.
hasEmailAddressBeenUsed(String) - Method in interface net.sourceforge.seqware.common.business.RegistrationService
hasEmailAddressBeenUsed.
hasExpiryTime() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
hasExpiryTime() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
hasExpiryTime() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
 
hasFeatureSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
hasFeatureSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
hasFeatureSet() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
hasFirstName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
hasFirstName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
hasFirstName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
hasFork() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
hasFriendlyRowkey() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
hasFriendlyRowkey() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
hasFriendlyRowkey() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
 
hasGrp() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
hasGrp() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
hasGrp() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
 
hashCode() - Method in class com.github.seqware.queryengine.kernel.RPNStack.Parameter
 
hashCode() - Method in class com.github.seqware.queryengine.model.Feature
hashCode() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
hashCode() - Method in class com.github.seqware.queryengine.model.impl.FeatureList
hashCode() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
hashCode() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
hashCode() - Method in class com.github.seqware.queryengine.model.Tag
hashCode() - Method in class com.github.seqware.queryengine.model.User
hashCode() - Method in class com.github.seqware.queryengine.util.LazyReference
hashCode() - Method in class com.github.seqware.queryengine.util.SGID
hashCode() - Method in class net.sourceforge.seqware.common.model.Expense
hashCode() - Method in class net.sourceforge.seqware.common.model.Experiment
hashCode() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
hashCode() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
hashCode.
hashCode() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
hashCode.
hashCode() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
hashCode() - Method in class net.sourceforge.seqware.common.model.File
hashCode() - Method in class net.sourceforge.seqware.common.model.FileType
hashCode() - Method in class net.sourceforge.seqware.common.model.Invoice
hashCode() - Method in class net.sourceforge.seqware.common.model.IUS
hashCode() - Method in class net.sourceforge.seqware.common.model.Lane
hashCode() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
hashCode() - Method in class net.sourceforge.seqware.common.model.LibrarySource
hashCode() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
hashCode() - Method in class net.sourceforge.seqware.common.model.Organism
hashCode.
hashCode() - Method in class net.sourceforge.seqware.common.model.Platform
hashCode() - Method in class net.sourceforge.seqware.common.model.Processing
hashCode() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
hashCode() - Method in class net.sourceforge.seqware.common.model.Project
hashCode() - Method in class net.sourceforge.seqware.common.model.Registration
hashCode.
hashCode() - Method in class net.sourceforge.seqware.common.model.Sample
hashCode() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
hashCode() - Method in class net.sourceforge.seqware.common.model.SequencerRun
hashCode() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
hashCode() - Method in class net.sourceforge.seqware.common.model.ShareStudy
hashCode() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
hashCode() - Method in class net.sourceforge.seqware.common.model.Study
hashCode() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
hashCode() - Method in class net.sourceforge.seqware.common.model.StudyType
hashCode() - Method in class net.sourceforge.seqware.common.model.Workflow
hashCode() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
hashCode() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
hashCode() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
hashCode() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
hashCode.
hashCode() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
hashCode() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
hashCode() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
 
hashCode() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
hashCode() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
 
hasId() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasId() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasId() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasJoin() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
hasKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasKey() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasLastName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
hasLastName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
hasLastName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
hasLeastSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
hasLeastSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
hasLeastSigBits() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
 
hasMetadataWriteback() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
hasMetadataWriteback() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
hasMetadataWriteback - Variable in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
hasMetadataWriteback() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
hasMetadataWriteback() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
job specific metadata is not supported yet
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginPBOrBuilder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginRunPBOrBuilder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
hasMostSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
hasMostSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
hasMostSigBits() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
hasName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
hasName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginPBOrBuilder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
hasName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
hasName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
hasName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
hasNameBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
hasNameBeenUsed.
hasNameBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
hasNameBeenUsed.
hasNameBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
hasNameBeenUsed.
hasNameBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
hasNameBeenUsed.
hasNameBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.LaneService
hasNameBeenUsed.
hasNameBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.ProjectService
hasNameBeenUsed.
hasNameBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.SampleService
hasNameBeenUsed.
hasNameBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
hasNameBeenUsed.
hasNext() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.FeatureScanIterator
 
hasNext() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterator
 
hasNext() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl.TagValueIterator
 
hasNext() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.BatchedRowFeatureListsIterator
 
hasNext() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.ConsolidatedFeatureIterator
 
hasNext() - Method in class com.github.seqware.queryengine.util.SeqWareIterator
Super method for dealing with database iterator specifics, such as closing the DB-iterator when no more data is available.
hasNext() - Method in class com.github.seqware.queryengine.util.SGIDIterable.SGIDIterator
 
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator
hasNext.
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator
hasNext.
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator
hasNext.
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.LocatableSecondaryCursorIterator
hasNext.
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator
hasNext.
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator
hasNext.
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator
hasNext.
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator
hasNext.
hasNextImpl() - Method in class com.github.seqware.queryengine.util.InMemoryIterator
Implementation of hasNext().
hasNextImpl() - Method in class com.github.seqware.queryengine.util.SeqWareIterator
Implementation of hasNext().
hasOrganism() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
hasOrganism() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
hasOrganism() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
hasParameters() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
hasParameters() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
hasParameters() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginRunPBOrBuilder
 
hasPassword() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
hasPassword() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
hasPassword() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
hasPhase() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasPhase() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasPhase() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasPragma() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasPragma() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasPragma() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
hasPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
hasPrecedingID() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
hasPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
hasPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
hasPrecedingID() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginPBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.PluginRunPBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
 
hasPredicate() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasPredicate() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasPredicate() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasProperty(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
hasPropertyAndNotNull(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
hasReferenceID() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
hasReferenceID() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
hasReferenceID() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
 
hasRefName() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
hasRefName() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
hasRefName() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
hasRequiredValues() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
hasRowKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
hasRowKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
hasRowKey() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
hasScore() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasScore() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasScore() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
hasSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
hasSerializationConstant() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
hasSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
hasSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
hasSerializationConstant() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
hasSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
hasSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
hasSgid() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
 
hasSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
hasSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
hasSgid() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
 
hasSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
hasSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
hasSgid() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
hasSource() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasSource() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasSource() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasStart() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasStart() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasStart() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasStop() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasStop() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasStop() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasStrand() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasStrand() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasStrand() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasTagSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasTagSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasTagSet() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasTimestamp() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
hasTimestamp() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
hasTimestamp() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
 
hasTitleBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
hasTitleBeenUsed.
hasTitleBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
hasTitleBeenUsed.
hasTitleBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
hasTitleBeenUsed.
hasTitleBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.StudyService
hasTitleBeenUsed.
hasTombstone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
hasTombstone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
hasTombstone() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
 
hasType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
hasType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
hasType() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
 
hasUser() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
hasUser() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
hasUser() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
 
hasVariable(String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.StringUtils
check if a string has FTL style variables ${variable}
hasVBytes() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasVBytes() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasVBytes() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasVDouble() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasVDouble() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasVDouble() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasVFloat() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasVFloat() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasVFloat() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasVInteger() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasVInteger() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasVInteger() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasVLong() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasVLong() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasVLong() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasVSGIDRef() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasVSGIDRef() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasVSGIDRef() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
hasVString() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
hasVString() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
hasVString() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
 
HBaseModelIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators
FIXME: need to create a locatable model iterator and then pass in the end point, otherwise the code that uses this object will need to do bounds checking!
HBaseModelIterator(ResultScanner, HTable, TupleBinding, String, String, boolean) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator
Constructor for HBaseModelIterator.
HBaseModelManager - Class in com.github.seqware.queryengine.impl
A Simple implementation of the CreateUpdateManager interface.
HBaseModelManager() - Constructor for class com.github.seqware.queryengine.impl.HBaseModelManager
 
HBasePersistentBackEnd - Class in com.github.seqware.queryengine.impl
Implement HBase optimizations for the back-end
HBasePersistentBackEnd(StorageInterface) - Constructor for class com.github.seqware.queryengine.impl.HBasePersistentBackEnd
Constructor for HBasePersistentBackEnd.
HBaseRead2 - Class in net.sourceforge.seqware.queryengine.prototypes.hadoop
HBaseRead2 class.
HBaseRead2() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.hadoop.HBaseRead2
 
HBaseReadWriteExample - Class in net.sourceforge.seqware.queryengine.prototypes.hadoop
HBaseReadWriteExample class.
HBaseReadWriteExample() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.hadoop.HBaseReadWriteExample
 
HBaseStorage - Class in com.github.seqware.queryengine.impl
HBaseStorage class.
HBaseStorage(SerializationInterface) - Constructor for class com.github.seqware.queryengine.impl.HBaseStorage
Constructor for HBaseStorage.
HBaseStorage.FeatureScanIterable - Class in com.github.seqware.queryengine.impl
A scanner specifically for Features.
HBaseStorage.FeatureScanIterable(ResultScanner, SGID) - Constructor for class com.github.seqware.queryengine.impl.HBaseStorage.FeatureScanIterable
 
HBaseStorage.FeatureScanIterator - Class in com.github.seqware.queryengine.impl
Presents an interface for iterating through FeatureLists
HBaseStorage.FeatureScanIterator(ResultScanner, SGID) - Constructor for class com.github.seqware.queryengine.impl.HBaseStorage.FeatureScanIterator
 
HBaseStorage.ScanIterable - Class in com.github.seqware.queryengine.impl
A generic scanner
HBaseStorage.ScanIterable(ResultScanner, Class) - Constructor for class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterable
 
HBaseStorage.ScanIterator - Class in com.github.seqware.queryengine.impl
Presents an interface for iterating through SGIDs
HBaseStorage.ScanIterator(ResultScanner, Class) - Constructor for class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterator
 
HBaseStore - Class in net.sourceforge.seqware.queryengine.backend.store.impl
HBaseStore class.
HBaseStore() - Constructor for class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
HBaseTagModelIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators
HBaseTagModelIterator class.
HBaseTagModelIterator(String, ResultScanner, HTable, TupleBinding, String, String) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator
Constructor for HBaseTagModelIterator.
helicos - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
 
hello(int) - Method in class net.sourceforge.seqware.webservice.resources.queries.SequencerRunIdFilesResource
hello.
hello(int) - Method in class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesResource
hello.
hello(int) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIdFilesResource
hello.
HelloWorld - Class in net.sourceforge.seqware.pipeline.plugins
HelloWorld class.
HelloWorld() - Constructor for class net.sourceforge.seqware.pipeline.plugins.HelloWorld
Constructor for HelloWorld.
HEMIZYGOUS - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant HEMIZYGOUS=3
HETEROZYGOUS - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant HETEROZYGOUS=2
HG_19 - Static variable in class com.github.seqware.queryengine.tutorial.Poster
Constant HG_19="hg_19"
HG_19 - Static variable in class com.github.seqware.queryengine.tutorial.PosterSGE
Constant HG_19="hg_19"
hibernateCalls() - Method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions
hibernateCalls.
high_precedence_constraint() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
high_precedence_constraint.
hold - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
 
holdForPeriod - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
 
holdUntilDate - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
 
HOMOZYGOUS - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant HOMOZYGOUS=1
HOST - Static variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
 
hostname - Variable in class net.sourceforge.seqware.common.util.filetools.FileTools.LocalhostPair
 
HTMLTagValidator - Class in net.sourceforge.solexatools.util
HTMLTagValidator class.
HTMLTagValidator() - Constructor for class net.sourceforge.solexatools.util.HTMLTagValidator
Constructor for HTMLTagValidator.
hybridassembly - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
 

I

ID - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant ID=13
ID - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant ID=13
id - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
id - Variable in class net.sourceforge.seqware.queryengine.backend.model.Model
 
id - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
 
id - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
 
id - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
 
id - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK
 
id - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
 
id - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
 
ID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
identifier() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
identifier.
illumina - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
 
impersonate(SGID) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Set the UUID, very dangerous, this should never be called outside of the backend
impersonate(SGID, SGID) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Set the UUID, very dangerous, this should never be called outside of the backend
ImportConstants - Class in com.github.seqware.queryengine.system.importers.workers
Noticed that a few of the file types repeat a lot of information that we might want to store as fields (and are fields in the old prototype).
ImportConstants() - Constructor for class com.github.seqware.queryengine.system.importers.workers.ImportConstants
 
Importer - Class in com.github.seqware.queryengine.system.importers
This looks like a class to control concurrency for multiple ImportWorkers, one per input file
Importer(int) - Constructor for class com.github.seqware.queryengine.system.importers.Importer
Constructor for Importer.
Importer() - Constructor for class com.github.seqware.queryengine.system.importers.Importer
Constructor for Importer.
Importer - Class in net.sourceforge.seqware.queryengine.tools.importers
Importer class.
Importer(int) - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.Importer
Constructor for Importer.
Importer() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.Importer
Constructor for Importer.
ImporterTest - Class in net.sourceforge.seqware.queryengine.prototypes.hadoop
ImporterTest class.
ImporterTest() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.hadoop.ImporterTest
 
ImporterTest2 - Class in net.sourceforge.seqware.queryengine.prototypes.hadoop
ImporterTest2 class.
ImporterTest2() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.hadoop.ImporterTest2
 
ImportWorker - Class in com.github.seqware.queryengine.system.importers.workers
Base Worker class, looks like a Bean for storing settings about the file to be converted.
ImportWorker() - Constructor for class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Constructor for ImportWorker.
ImportWorker(String, Importer, String, boolean, int, int, float, boolean, int, boolean, boolean, int) - Constructor for class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Constructor for ImportWorker.
ImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
ImportWorker class.
ImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Constructor for ImportWorker.
ImportWorker(String, Importer, Store, String, boolean, int, int, float, boolean, int, boolean, boolean, int) - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Constructor for ImportWorker.
includeCoverage - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
includeIndels - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
includeSNV - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
incrementCounter() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner.PluginRunnerMapper
 
incrementCounter() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryPluginRunner
 
incrementCounter() - Method in interface com.github.seqware.queryengine.plugins.MapperInterface
 
indirectBIMap - Variable in class com.github.seqware.queryengine.backInterfaces.StorageInterface
These tables are created on-the-fly with a referenceID appended in order to separate out Features by Reference
info(Object) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.info(Object).
info(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.info(Object,Throwable).
informOnError - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
 
informOnStatus - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
 
ini2Map(String, Map<String, String>) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools
ini2Map.
ini2Map(String, Map<String, String>, boolean) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools
ini2Map.
ini2Map(InputStream, Map<String, String>, boolean) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools
ini2Map.
ini2RichMap(String, Map<String, Map<String, String>>) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools
This is a little different than the ini2Map since it allows us to read ini files where key-value annotations on the key-values appear in comments on the previous line above the current such as: key=bam_inputs:type=file:display=T:display_name=BAM Input(s):file_meta_type=application/bam or key=run_ends:type=pulldown:display=T:display_name=Single or Paired Ends:pulldown_items=Single End|1;Paired End|2 The extra information is used by the Portal and Web Service to display interfaces that let people call the workflows correctly.
iniString2Map(String) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools
iniString2Map.
init(FeatureSet, Object...) - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
 
init(FeatureSet, Object...) - Method in interface com.github.seqware.queryengine.plugins.PluginInterface
Initialize this plug-in, this is called once when the plug-in is starting a job
init(String, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
init.
init(DataSource) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
Connect to a database for future use
init(String, String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
init.
init(String, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
init.
init(String, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
init.
init() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider
Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
init() - Method in class net.sourceforge.seqware.pipeline.module.Module
init.
init() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
Module initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
init.
init() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
 
init() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator
Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection
Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager
Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker
Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker
 
init() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner
Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.OozieXML2Dot
 
init() - Method in class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot
 
init() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter
Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter
Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter
Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
Plugin initialization code goes here.
init(Request) - Method in class net.sourceforge.seqware.webservice.resources.BasicRestlet
init.
initBinder(HttpServletRequest, ServletRequestDataBinder) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
InMemoryFeatureSet - Class in com.github.seqware.queryengine.model.impl.inMemory
An in-memory representation of a feature set.
InMemoryFeatureSet.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
 
InMemoryFeatureSet.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet.Builder
 
InMemoryGroup - Class in com.github.seqware.queryengine.model.impl.inMemory
An in-memory representation of a group.
InMemoryGroup() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
 
InMemoryGroup.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
 
InMemoryGroup.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup.Builder
 
InMemoryIterable<T> - Class in com.github.seqware.queryengine.util
A bit of a hack class, allows us to have getCount as well as iterable
InMemoryIterable(Collection) - Constructor for class com.github.seqware.queryengine.util.InMemoryIterable
Constructor for InMemoryIterable.
InMemoryIterator<T> - Class in com.github.seqware.queryengine.util
An in-memory iterator for unit testing of SeqWareIterator.
InMemoryIterator(Iterator<T>) - Constructor for class com.github.seqware.queryengine.util.InMemoryIterator
Creates a new in-memory SeqWareIterator implementation.
InMemoryPlugin - Class in com.github.seqware.queryengine.model.impl.inMemory
An in-memory representation of a Plugin.
InMemoryPlugin() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryPlugin
 
InMemoryPlugin.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
 
InMemoryPlugin.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryPlugin.Builder
 
InMemoryPluginRunner<ResultType> - Class in com.github.seqware.queryengine.plugins.inmemory
Base class for all in-memory plug-in runners.
InMemoryPluginRunner(PluginInterface, FeatureSet, Object[]) - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryPluginRunner
 
InMemoryReference - Class in com.github.seqware.queryengine.model.impl.inMemory
An in-memory representation of a reference.
InMemoryReference() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference
Anonymous constructor
InMemoryReference.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
 
InMemoryReference.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference.Builder
 
InMemoryReferenceSet - Class in com.github.seqware.queryengine.model.impl.inMemory
An in-memory representation of a reference set.
InMemoryReferenceSet() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet
 
InMemoryReferenceSet.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
 
InMemoryReferenceSet.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet.Builder
 
InMemoryTagSet - Class in com.github.seqware.queryengine.model.impl.inMemory
An in-memory representation of a TagSet.
InMemoryTagSet() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
 
InMemoryTagSet.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
 
InMemoryTagSet.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet.Builder
 
input - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
INPUT_FILE_FILE_PATHS - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
INPUT_FILE_META_TYPES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
INPUT_FILE_SWIDS - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
INPUT_FILES_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
Constant INPUT_FILES_PARAM='i'
inputFile - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
inputFile - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
inputFile - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
inputFile - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
inputFile - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
inputSize - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
insert(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
insert.
insert(Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
insert.
insert(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
insert.
insert(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
insert.
insert(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService
insert.
insert(File) - Method in interface net.sourceforge.seqware.common.business.FileService
insert.
insert(Registration, File) - Method in interface net.sourceforge.seqware.common.business.FileService
insert.
insert(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl
insert.
insert(Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
insert.
insert(Registration, Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
insert.
insert(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl
insert.
insert(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl
insert.
insert(File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
insert.
insert(Registration, File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
insert.
insert(Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
Inserts a new Invoice and returns its sw_accession number.
insert(Registration, Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
insert.
insert(IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
insert.
insert(Registration, IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
insert.
insert(Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
insert.
insert(Registration, Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
insert.
insert(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
insert.
insert(ProcessingIus) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
insert.
insert(ProcessingLanes) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
insert.
insert(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
insert.
insert(ProcessingSamples) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
insert.
insert(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
insert.
insert(SequencerRun, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
insert.
insert(Registration, SequencerRun, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
insert.
insert(Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
Inserts a new Processing and returns its sw_accession number.
insert(Registration, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
insert.
insert(ProcessingStudies) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
insert.
insert(Project) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
insert.
insert(RegistrationDTO) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
insert.
insert(String[], InvitationParams, MailSender) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
insert.
insert(Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
insert.
insert(Registration, Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
insert.
insert(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
insert.
insert(SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
This is being used to create a new SequencerRun object and the correct number of assocated Lanes
insert(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
insert.
insert(Registration, SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
insert.
insert(ShareExperiment) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
insert.
insert(ShareFile) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
insert.
insert(ShareLane) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
insert.
insert(ShareProcessing) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
insert.
insert(ShareSample) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
insert.
insert(ShareStudy) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
insert.
insert(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
insert.
insert(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
insert.
insert(Registration, Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
insert.
insert(StudyType) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
insert.
insert(WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
Inserts a new WorkflowParam and returns its primary key.
insert(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
insert.
insert(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
Inserts a new WorkflowParamValue and returns its primary key.
insert(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
insert.
insert(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
insert.
insert(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
insert.
insert(WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
Inserts a new WorkflowRun and returns its sw_accession number.
insert(WorkflowRun, SortedSet<WorkflowRunParam>, Map<String, List<File>>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
insert.
insert(Registration, WorkflowRun, SortedSet<WorkflowRunParam>, Map<String, List<File>>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
insert.
insert(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
insert.
insert(Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
Inserts a new Workflow and returns its sw_accession number.
insert(Registration, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
insert.
insert(Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
Inserts a new Invoice and returns its sw_accession number.
insert(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
insert.
insert(IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService
insert.
insert(Registration, IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService
insert.
insert(Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService
insert.
insert(Registration, Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService
insert.
insert(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService
insert.
insert(ProcessingIus) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService
insert.
insert(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService
insert.
insert(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService
insert.
insert(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService
insert.
insert(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService
insert.
insert(SequencerRun, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
insert.
insert(Registration, SequencerRun, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
insert.
insert(Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
Inserts a new Processing and returns its sw_accession number.
insert(Registration, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
insert.
insert(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService
insert.
insert(Project) - Method in interface net.sourceforge.seqware.common.business.ProjectService
insert.
insert(RegistrationDTO) - Method in interface net.sourceforge.seqware.common.business.RegistrationService
insert.
insert(String[], InvitationParams, MailSender) - Method in interface net.sourceforge.seqware.common.business.RegistrationService
insert.
insert(Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService
insert.
insert(Registration, Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService
insert.
insert(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
insert.
insert(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
insert.
insert(SequencerRunWizardDTO) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
insert.
insert(Registration, SequencerRunWizardDTO) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
insert.
insert(ShareExperiment) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
insert.
insert(ShareFile) - Method in interface net.sourceforge.seqware.common.business.ShareFileService
insert.
insert(ShareLane) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
insert.
insert(ShareProcessing) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
insert.
insert(ShareSample) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
insert.
insert(ShareStudy) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
insert.
insert(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
insert.
insert(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
insert.
insert(Registration, Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
insert.
insert(StudyType) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService
insert.
insert(WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
Inserts a new WorkflowParam and returns its primary key.
insert(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
insert.
insert(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
Inserts a new WorkflowParamValue and returns its primary key.
insert(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
insert.
insert(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
insert.
insert(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
insert.
insert(WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
Inserts a new WorkflowRun and returns its sw_accession number.
insert(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
insert.
insert(WorkflowRun, SortedSet<WorkflowRunParam>, Map<String, List<File>>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
insert.
insert(Registration, WorkflowRun, SortedSet<WorkflowRunParam>, Map<String, List<File>>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
insert.
insert(Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
Inserts a new Workflow and returns its sw_accession number.
insert(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
insert.
insert(ExperimentAttribute) - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO
insert.
insert(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
insert.
insert(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
insert.
insert(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO
insert.
insert(ExperimentLink) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO
insert.
insert(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO
insert.
insert(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO
insert.
insert(File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
insert.
insert(Registration, File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
insert.
insert(ExperimentAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate
insert.
insert(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
insert.
insert(Registration, Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
insert.
insert(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate
insert.
insert(ExperimentLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate
insert.
insert(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate
insert.
insert(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate
insert.
insert(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
insert.
insert(Registration, File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
insert.
insert(Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
Inserts a new Invoice and returns its sw_accession number.
insert(Registration, Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
insert.
insert(IUSAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate
insert.
insert(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
insert.
insert(Registration, IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
insert.
insert(IUSLink) - Method in interface net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAO
insert.
insert(IUSLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate
insert.
insert(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAO
insert.
insert(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate
insert.
insert(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
insert.
insert(Registration, Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
insert.
insert(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAO
insert.
insert(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate
insert.
insert(ProcessingAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate
insert.
insert(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
Inserts a new Processing and returns its sw_accession number.
insert(Registration, Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
insert.
insert(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate
insert.
insert(ProcessingIus) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate
insert.
insert(ProcessingLanes) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate
insert.
insert(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate
insert.
insert(ProcessingSamples) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate
insert.
insert(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate
insert.
insert(ProcessingStudies) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate
insert.
insert(Project) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate
insert.
insert(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate
insert.
insert(SampleAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate
insert.
insert(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
insert.
insert(Registration, Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
insert.
insert(SampleLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate
insert.
insert(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
insert.
insert(SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
insert.
insert(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
insert.
insert(Registration, SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
insert.
insert(ShareExperiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
insert.
insert(ShareFile) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
insert.
insert(ShareLane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
insert.
insert(ShareProcessing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
insert.
insert(ShareSample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
insert.
insert(ShareStudy) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate
insert.
insert(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
insert.
insert(StudyAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate
insert.
insert(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
insert.
insert(Registration, Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
insert.
insert(StudyLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate
insert.
insert(StudyType) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate
insert.
insert(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
Inserts a new Workflow and returns its sw_accession number.
insert(Registration, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
insert.
insert(WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
Inserts a new WorkflowParam and returns its primary key.
insert(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
insert.
insert(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
Inserts a new WorkflowParamValue and returns its primary key.
insert(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
insert.
insert(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
Inserts a new WorkflowRun and returns its sw_accession number.
insert(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
insert.
insert(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
insert.
insert(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
insert.
insert(Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
Inserts a new Invoice and returns its sw_accession number.
insert(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
insert.
insert(IUSAttribute) - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO
insert.
insert(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
insert.
insert(Registration, IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
insert.
insert(Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
insert.
insert(Registration, Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
insert.
insert(ProcessingAttribute) - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO
insert.
insert(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
Inserts a new Processing and returns its sw_accession number.
insert(Registration, Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
insert.
insert(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO
insert.
insert(ProcessingIus) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO
insert.
insert(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO
insert.
insert(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO
insert.
insert(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO
insert.
insert(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO
insert.
insert(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO
insert.
insert(Project) - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO
insert.
insert(Registration) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO
insert.
insert(SampleAttribute) - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO
insert.
insert(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
insert.
insert(Registration, Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
insert.
insert(SampleLink) - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO
insert.
insert(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
insert.
insert(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
insert.
insert(SequencerRunWizardDTO) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
insert.
insert(Registration, SequencerRunWizardDTO) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
insert.
insert(ShareExperiment) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO
insert.
insert(ShareFile) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO
insert.
insert(ShareLane) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO
insert.
insert(ShareProcessing) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO
insert.
insert(ShareSample) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO
insert.
insert(ShareStudy) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO
insert.
insert(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
insert.
insert(StudyAttribute) - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO
insert.
insert(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
insert.
insert(Registration, Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
insert.
insert(StudyLink) - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO
insert.
insert(StudyType) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO
insert.
insert(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
Inserts a new Workflow and returns its sw_accession number.
insert(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
insert.
insert(WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO
Inserts a new WorkflowParam and returns its primary key.
insert(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO
insert.
insert(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
Inserts a new WorkflowParamValue and returns its primary key.
insert(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
insert.
insert(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
Inserts a new WorkflowRun and returns its sw_accession number.
insert(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
insert.
insert(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
insert.
insert(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
insert.
InsertAndReturnNewPrimaryKey(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
Find out the primary key for the last inserted record FIXME: This is hardcoded for Postgres, need to make DB agnostic
InsertAndReturnNewPrimaryKey(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
Find out the primary key for the last inserted record FIXME: This is hardcoded for Postgres, need to make DB agnostic
insertFilesAsWorkflowRunParam(WorkflowRun, Map<String, List<File>>) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
insertFilesAsWorkflowRunParam.
insertFilesAsWorkflowRunParam(Registration, WorkflowRun, Map<String, List<File>>) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
insertFilesAsWorkflowRunParam.
insertFilesAsWorkflowRunParam(WorkflowRun, Map<String, List<File>>) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
insertFilesAsWorkflowRunParam.
insertFilesAsWorkflowRunParam(Registration, WorkflowRun, Map<String, List<File>>) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
insertFilesAsWorkflowRunParam.
INSERTION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant INSERTION=2
insertLane(Registration, Sample, UploadSequence, FileType) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
insertLane.
insertLane(Registration, Sample, UploadSequence, FileType) - Method in interface net.sourceforge.seqware.common.business.LaneService
insertLane.
insertWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource
insertWorkflowRun.
InSessionExecutions - Class in net.sourceforge.seqware.common.hibernate
Abstract InSessionExecutions class.
InSessionExecutions() - Constructor for class net.sourceforge.seqware.common.hibernate.InSessionExecutions
 
installBundle(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
installBundle.
installBundle(File, File, boolean, boolean) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
This method allows you to install the workflow bundle to the metadb optionally building a zip file along the way and archiving it to a safe location.
installBundleDirOnly(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
installBundleDirOnly.
installBundleZipOnly(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
installBundleZipOnly.
installPlugin(PluginInterface) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
Install a plug-in so that it can be listed
installPlugin(PluginInterface) - Method in interface com.github.seqware.queryengine.model.QueryInterface
Install a plug-in so that it can be listed
instance - Static variable in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter
 
instanceOf(Object, String) - Static method in class net.sourceforge.solexatools.util.TagUtils
instanceOf.
instrumentmodel - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
 
instrumentmodel - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
 
instrumentmodel - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
 
instrumentmodel - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
 
instrumentModel - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
instrumentName - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
INT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant INT=14
INT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant INT=14
INT_PARAMETERS - Static variable in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner
Constant INT_PARAMETERS="int_parameters"
int_parameters - Variable in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner.PluginRunnerMapper
parameters that will be handled by the plug-in developer but will not be available to the user of the plug-in
IntegerIdComparator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators
IntegerIdComparator class.
IntegerIdComparator() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators.IntegerIdComparator
 
interactive - Variable in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
internalGetValueMap() - Static method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
INVALID_ID - Static variable in class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
 
INVALID_INPUT - Static variable in class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
 
INVALID_SET - Static variable in class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
 
INVALIDARGUMENT - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant INVALIDARGUMENT=9
INVALIDFILE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant INVALIDFILE=7
InvalidIDException - Exception in com.github.seqware.queryengine.system.rest.exception
 
InvalidIDException(int, String) - Constructor for exception com.github.seqware.queryengine.system.rest.exception.InvalidIDException
 
INVALIDPARAMETERS - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant INVALIDPARAMETERS=2
INVALIDPLUGIN - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant INVALIDPLUGIN=120
InvitationParams - Class in net.sourceforge.seqware.common.invitation
InvitationParams class.
InvitationParams(String, String, String) - Constructor for class net.sourceforge.seqware.common.invitation.InvitationParams
Constructor for InvitationParams.
InviteNewUserController - Class in net.sourceforge.solexatools.webapp.controller
InviteNewUserController class.
InviteNewUserController() - Constructor for class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
Constructor for InviteNewUserController.
InviteNewUserSetupController - Class in net.sourceforge.solexatools.webapp.controller
InviteNewUserSetupController class.
InviteNewUserSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.InviteNewUserSetupController
Constructor for InviteNewUserSetupController.
InviteNewUserValidatorController - Class in net.sourceforge.solexatools.webapp.controller
InviteNewUserValidatorController class.
InviteNewUserValidatorController() - Constructor for class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController
Constructor for InviteNewUserValidatorController.
Invoice - Class in net.sourceforge.seqware.common.model
Invoice class.
Invoice() - Constructor for class net.sourceforge.seqware.common.model.Invoice
Constructor for Invoice.
InvoiceDAO - Interface in net.sourceforge.seqware.common.dao
InvoiceDAO interface.
InvoiceDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
InvoiceDAOHibernate class.
InvoiceDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
Constructor for InvoiceDAOHibernate.
InvoiceDetailsController - Class in net.sourceforge.solexatools.webapp.controller
InvoiceDetailsController class.
InvoiceDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController
Constructor for InvoiceDetailsController.
InvoiceService - Interface in net.sourceforge.seqware.common.business
InvoiceService interface.
invoiceService - Variable in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController
 
invoiceService - Variable in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController
 
InvoiceServiceImpl - Class in net.sourceforge.seqware.common.business.impl
InvoiceServiceImpl class.
InvoiceServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
Constructor for InvoiceServiceImpl.
isActiveTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
isActiveTransaction.
isActiveTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
isActiveTransaction.
isActiveTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
isActiveTransaction.
isActiveTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
isActiveTransaction.
isActiveTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
isActiveTransaction.
isAuthenticated(HttpServletRequest) - Static method in class net.sourceforge.solexatools.Security
isAuthenticated.
isCheckEmail(String) - Static method in class net.sourceforge.solexatools.validation.LoginValidator
isCheckEmail.
isComplete() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner
 
isComplete() - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
 
isComplete() - Method in interface com.github.seqware.queryengine.plugins.PluginInterface
Non-blocking call to determine whether the result is ready
isCompressed() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
isCompressed.
isCompressed() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
isCompressed.
isConfigError(Throwable) - Method in class net.sourceforge.solexatools.authentication.UNCKerberos
isConfigError.
isCountAsFail(BasicDecider.FILE_STATUS, BasicDecider.PREVIOUS_RUN_STATUS) - Static method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
We now use the guideline that we only count failures when they occur on the same number of files (with the same paths)
isCreateConsequenceAnnotationDB() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
isCreateConsequenceAnnotationDB.
isCreateCoverageDB() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
isCreateCoverageDB.
isCreateDbSNPAnnotationDB() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
isCreateDbSNPAnnotationDB.
isCreateMismatchDB() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
isCreateMismatchDB.
isDebug() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareBase
isDebug.
isDescendantOf(String) - Method in class com.github.seqware.queryengine.model.Tag
Tests whether the given tag is a parent of this tag -- making this tag a descendant of the parameter tag.
isDisplay() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
isDisplay.
isDone() - Method in class com.github.seqware.queryengine.model.PluginRun
Returns true iff the query is ready with its results.
isDone() - Method in interface com.github.seqware.queryengine.model.QueryFuture
Returns true iff the query is ready with its results.
isDoRerun(BasicDecider.FILE_STATUS, BasicDecider.PREVIOUS_RUN_STATUS) - Static method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
We want to re-run in a variety of conditions.
isDuplicateFile(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
isDuplicateFile.
isDuplicateFile(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
isDuplicateFile.
isDuplicateFile(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
isDuplicateFile.
isDuplicateFile(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
isDuplicateFile.
isEnd() - Method in class net.sourceforge.solexatools.util.PageInfo
isEnd.
isExists(String, String) - Method in interface net.sourceforge.seqware.common.business.FileService
isExists.
isExists(String, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
isExists.
isExistsShare(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
isExistsShare.
isExistsShare(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
isExistsShare.
isExistsShare(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
isExistsShare.
isExistsShare(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
isExistsShare.
isExpires() - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl
Return true iff this expires
isExpires() - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable
Return true iff this expires
isFileOwner(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
This tool uses the 'whoami' and 'stat' commands to verify if the current users running this program is the owner for the specified file or directory.
isFinalized() - Method in class net.sourceforge.seqware.common.model.Invoice
isFinalized.
isForceCopy() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
 
isFullyPaid() - Method in class net.sourceforge.seqware.common.model.Invoice
isFullyPaid.
isGcrSkipIfMissing() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
 
isGcrSkipIfOutputExists() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
 
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService
isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.IUSService
isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService
isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.LaneService
isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService
isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.SampleService
isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService
isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.StudyService
isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
isHasFile.
isIncludeCoverage() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
isIncludeCoverage.
isIncludeCoverage() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
isIncludeCoverage.
isIncludeIndels() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
isIncludeIndels.
isIncludeIndels() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
isIncludeIndels.
isIncludeIndels() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
isIncludeIndels.
isIncludeSNV() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
isIncludeSNV.
isIncludeSNV() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
isIncludeSNV.
isIncludeSNVs() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
isIncludeSNVs.
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
isInput() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
is an input file?
isInstalled() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
 
isJoinDevelopersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration
isJoinDevelopersMailingList.
isJoinUsersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration
isJoinUsersMailingList.
isLaunch() - Method in class net.sourceforge.seqware.common.model.Workflow
isLaunch.
isLIMSAdmin() - Method in class net.sourceforge.seqware.common.model.Registration
isLIMSAdmin.
isLocal() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
isLocal() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
Whether this job should run locally instead of out on a cluster.
isLocked() - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
Deprecated. isLocked.
isMetadataWriteBack() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
need metadata writeback? user can override this setting by using --no-metadata or --metadata from command line
isOutput() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
is an output file?
isPayee() - Method in class net.sourceforge.seqware.common.model.Registration
isPayee.
isPrivate() - Method in class net.sourceforge.seqware.common.model.Workflow
isPrivate.
isPublic() - Method in class net.sourceforge.seqware.common.model.Workflow
isPublic.
isReadOnly() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
isReadOnly.
isReportInputFiles() - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
isRequireFiles() - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
isRequireFiles.
isReturnIds() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
isReturnIds.
isSortable() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
isStart() - Method in class net.sourceforge.solexatools.util.PageInfo
isStart.
isTaskGroup() - Method in class net.sourceforge.seqware.common.model.Processing
isTaskGroup.
isTechnician() - Method in class net.sourceforge.seqware.common.model.Registration
isTechnician.
isTombstone() - Method in class com.github.seqware.queryengine.util.FSGID
Back-end method for Features stored within high capacity featuresets
isToRunContained(int, Collection<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
Returns true if the filesToRun are totally contained by the files associated with the files in a given workflowRunAcc
isUsePairedFile() - Method in class net.sourceforge.seqware.common.model.UploadSequence
isUsePairedFile.
isVerbose() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
isVerbose.
isWait() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
wait for the workflow to finished, user can override this by using --wait from command line
isWorkflowRunAncesstor() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
isWorkflowRunAncesstor() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
itemRgb - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
iterator() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.FeatureScanIterable
 
iterator() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterable
 
iterator() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl.TagValueIterable
 
iterator() - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
iterator() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
iterator() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
iterator() - Method in class com.github.seqware.queryengine.util.InMemoryIterable
iterator() - Method in class com.github.seqware.queryengine.util.SGIDIterable
IUS - Class in net.sourceforge.seqware.common.model
 
IUS() - Constructor for class net.sourceforge.seqware.common.model.IUS
Constructor for IUS.
IUS_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant IUS_ATTRIBUTES="Header.IUS_ATTRIBUTES.getTitle()"
IUS_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
Constant IUS_PREFIX="ius_"
IUS_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant IUS_SWA="Header.IUS_SWA.getTitle()"
IUS_TAG - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant IUS_TAG="Header.IUS_TAG.getTitle()"
IUS_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant IUS_TAG_PREFIX="Header.IUS_TAG_PREFIX.getTitle()"
IUSAttribute - Class in net.sourceforge.seqware.common.model
IusAttribute generated by hbm2java
IUSAttribute() - Constructor for class net.sourceforge.seqware.common.model.IUSAttribute
Constructor for IUSAttribute.
IUSAttribute(int, IUS) - Constructor for class net.sourceforge.seqware.common.model.IUSAttribute
Constructor for IUSAttribute.
IUSAttribute(int, IUS, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.IUSAttribute
Constructor for IUSAttribute.
IUSAttributeDAO - Interface in net.sourceforge.seqware.common.dao
IUSAttributeDAO interface.
IUSAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
IUSAttributeDAOHibernate class.
IUSAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate
 
IUSController - Class in net.sourceforge.solexatools.webapp.controller
IUSController class.
IUSController() - Constructor for class net.sourceforge.solexatools.webapp.controller.IUSController
Constructor for IUSController.
IUSController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.IUSController
Constructor for IUSController.
IUSDAO - Interface in net.sourceforge.seqware.common.dao
IUSDAO interface.
IUSDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
IUSDAOHibernate class.
IUSDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
Constructor for IUSDAOHibernate.
IusDto - Class in net.sourceforge.seqware.webservice.dto
 
IusDto() - Constructor for class net.sourceforge.seqware.webservice.dto.IusDto
 
IusFilesResource - Interface in net.sourceforge.seqware.webservice.resources.tables
IusFilesResource interface.
IusFilesServerResource - Class in net.sourceforge.seqware.webservice.resources.tables
IusFilesServerResource class.
IusFilesServerResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.IusFilesServerResource
Constructor for IusFilesServerResource.
IUSIDFilter - Class in net.sourceforge.seqware.webservice.resources.filters
IUSIDFilter class.
IUSIDFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.IUSIDFilter
 
IusIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
IusIDResource class.
IusIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.IusIDResource
Constructor for IusIDResource.
IUSLink - Class in net.sourceforge.seqware.common.model
IusLink generated by hbm2java
IUSLink() - Constructor for class net.sourceforge.seqware.common.model.IUSLink
Constructor for IUSLink.
IUSLink(int, IUS, String, String) - Constructor for class net.sourceforge.seqware.common.model.IUSLink
Constructor for IUSLink.
IUSLink(int, IUS, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.IUSLink
Constructor for IUSLink.
IUSLinkDAO - Interface in net.sourceforge.seqware.common.dao.hibernate
IUSLinkDAO interface.
IUSLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
IUSLinkDAOHibernate class.
IUSLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate
 
IUSList - Class in net.sourceforge.seqware.common.model.lists
IUSList class.
IUSList() - Constructor for class net.sourceforge.seqware.common.model.lists.IUSList
Constructor for IUSList.
IusResource - Class in net.sourceforge.seqware.webservice.resources.tables
IusResource class.
IusResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.IusResource
Constructor for IusResource.
IusSearchResource - Interface in net.sourceforge.seqware.webservice.resources.tables
IusSearchResource interface.
IusSearchServerResource - Class in net.sourceforge.seqware.webservice.resources.tables
IusSearchServerResource class.
IusSearchServerResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.IusSearchServerResource
Constructor for IusSearchServerResource.
IUSService - Interface in net.sourceforge.seqware.common.business
IUSService interface.
IUSServiceImpl - Class in net.sourceforge.seqware.common.business.impl
IUSServiceImpl class.
IUSServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
Constructor for IUSServiceImpl.
IUSSetupController - Class in net.sourceforge.solexatools.webapp.controller
IUSSetupController class.
IUSSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.IUSSetupController
 

J

JavaJob - Class in net.sourceforge.seqware.pipeline.workflowV2.model
 
JavaJob(String, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.JavaJob
 
JavaSeqwareModuleJob - Class in net.sourceforge.seqware.pipeline.workflowV2.model
 
JavaSeqwareModuleJob(String, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.JavaSeqwareModuleJob
 
JaxbObject<T> - Class in net.sourceforge.seqware.common.util.xmltools
Convenience class for converting objects into JAXB XML.
JaxbObject() - Constructor for class net.sourceforge.seqware.common.util.xmltools.JaxbObject
JAXB has a memory leak when it comes to making new JAXBContext instances, so one JAXBContext is created for the entire lifetime of the program and initialized with all of the classes that we marshal and unmarshal at the moment, as per the instructions at * http://whileonefork.blogspot.com/2010/09/leaking-of-jaxb.html and * http://jaxb.java.net/guide/Performance_and_thread_safety.html .
jdbcTemplate() - Method in class net.sourceforge.seqware.pipeline.runner.DefaultConfig
jdbcTemplate.
JndiDatasourceCreator - Class in net.sourceforge.seqware.common.util.testtools
JndiDatasourceCreator class.
JndiDatasourceCreator() - Constructor for class net.sourceforge.seqware.common.util.testtools.JndiDatasourceCreator
 
job - Variable in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner
 
Job - Interface in net.sourceforge.seqware.pipeline.workflowV2.model
 
JobModule - Class in net.sourceforge.seqware.pipeline.workflowV2.model
JobModule class.
JobModule(Module) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule
Constructor for JobModule.
jobObj - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
jobObj - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
JobProfile - Class in net.sourceforge.seqware.pipeline.workflowV2.model
JobProfile class.
JobProfile(String, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
Constructor for JobProfile.
JSON - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
Constant JSON="json"
JSON - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant JSON="json"
JsonUtil - Class in net.sourceforge.seqware.common.util.jsontools
JsonUtil class.
JsonUtil() - Constructor for class net.sourceforge.seqware.common.util.jsontools.JsonUtil
 

K

KEY_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
key_value_function() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
key_value_function.
keyIndex - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
keys() - Method in class net.sourceforge.seqware.pipeline.runner.RunnerParams
keys.
KEYVALUE_OUT_PARAM - Static variable in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper
Constant KEYVALUE_OUT_PARAM='k'
keyvalues - Variable in class net.sourceforge.seqware.queryengine.backend.model.Model
 
KryoSerialization - Class in com.github.seqware.queryengine.impl
KryoSerialization class.
KryoSerialization() - Constructor for class com.github.seqware.queryengine.impl.KryoSerialization
Constructor for KryoSerialization.

L

label - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
 
label - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
 
label - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK
 
label - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
 
label - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK
 
labName - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
Lane - Class in net.sourceforge.seqware.common.model
 
Lane() - Constructor for class net.sourceforge.seqware.common.model.Lane
Constructor for Lane.
LANE_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant LANE_ATTRIBUTES="Header.LANE_ATTRIBUTES.getTitle()"
LANE_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant LANE_NAME="Header.LANE_NAME.getTitle()"
LANE_NUM - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant LANE_NUM="Header.LANE_NUM.getTitle()"
LANE_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
Constant LANE_PREFIX="seq_"
LANE_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant LANE_SWA="Header.LANE_SWA.getTitle()"
LANE_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant LANE_TAG_PREFIX="Header.LANE_TAG_PREFIX.getTitle()"
LaneAttribute - Class in net.sourceforge.seqware.common.model
LaneAttribute generated by hbm2java
LaneAttribute() - Constructor for class net.sourceforge.seqware.common.model.LaneAttribute
Constructor for LaneAttribute.
LaneAttribute(int, Lane) - Constructor for class net.sourceforge.seqware.common.model.LaneAttribute
Constructor for LaneAttribute.
LaneAttribute(int, Lane, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.LaneAttribute
Constructor for LaneAttribute.
LaneAttributeDAO - Interface in net.sourceforge.seqware.common.dao.hibernate
LaneAttributeDAO interface.
LaneAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
LaneAttributeDAOHibernate class.
LaneAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate
 
LaneController - Class in net.sourceforge.solexatools.webapp.controller
LaneController
LaneController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneController
Constructor for LaneController.
LaneController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneController
Constructor for LaneController.
LaneDAO - Interface in net.sourceforge.seqware.common.dao
LaneDAO interface.
LaneDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
LaneDAOHibernate class.
LaneDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
Constructor for LaneDAOHibernate.
LaneIDFilter - Class in net.sourceforge.seqware.webservice.resources.filters
LaneIDFilter class.
LaneIDFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.LaneIDFilter
 
LaneIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
LaneIDResource class.
LaneIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LaneIDResource
Constructor for LaneIDResource.
LaneLink - Class in net.sourceforge.seqware.common.model
LaneLink generated by hbm2java
LaneLink() - Constructor for class net.sourceforge.seqware.common.model.LaneLink
Constructor for LaneLink.
LaneLink(int, Lane, String, String) - Constructor for class net.sourceforge.seqware.common.model.LaneLink
Constructor for LaneLink.
LaneLink(int, Lane, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.LaneLink
Constructor for LaneLink.
LaneLinkDAO - Interface in net.sourceforge.seqware.common.dao.hibernate
LaneLinkDAO interface.
LaneLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
LaneLinkDAOHibernate class.
LaneLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate
 
LaneList - Class in net.sourceforge.seqware.common.model.lists
LaneList class.
LaneList() - Constructor for class net.sourceforge.seqware.common.model.lists.LaneList
Constructor for LaneList.
LaneResource - Class in net.sourceforge.seqware.webservice.resources.tables
LaneResource class.
LaneResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LaneResource
Constructor for LaneResource.
LaneSampleAssociateController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
LaneSampleAssociateController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
Constructor for LaneSampleAssociateController.
LaneSampleAssociateSetupController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
LaneSampleAssociateSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
Constructor for LaneSampleAssociateSetupController.
LaneService - Interface in net.sourceforge.seqware.common.business
LaneService interface.
LaneServiceImpl - Class in net.sourceforge.seqware.common.business.impl
LaneServiceImpl class.
LaneServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
Constructor for LaneServiceImpl.
LaneSetupController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
LaneSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneSetupController
Constructor for LaneSetupController.
LaneValidator - Class in net.sourceforge.solexatools.validation
LaneValidator class.
LaneValidator() - Constructor for class net.sourceforge.solexatools.validation.LaneValidator
Constructor for LaneValidator.
LASTNAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
LAUNCH_SCHEDULED - Static variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
 
launchBundle(String, String, String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
launchBundle.
launchBundle(String, String, String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.WorkflowEngine
launchBundle.
launchInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
launchInstalledBundle.
launchInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.WorkflowEngine
launchInstalledBundle.
launchNewWorkflow(OptionSet, Map<String, String>, String[], Metadata, Integer, Integer) - Static method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
Separating out the launching of a new workflow.
launchScheduledBundle(String, String, boolean, boolean) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
launchScheduledBundle.
launchScheduledBundle(String, String, boolean, boolean) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.WorkflowEngine
launchScheduledBundle.
launchSingleWorkflow(boolean) - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
Processes a single workflow
launchWorkflow(AbstractWorkflowDataModel) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowEngine
launch the workflow according to the info filled in the input objectModel
launchWorkflow(AbstractWorkflowDataModel) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine
 
launchWorkflow(AbstractWorkflowDataModel) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.PegasusWorkflowEngine
 
LaunchWorkflowController - Class in net.sourceforge.solexatools.webapp.controller
LaunchWorkflowController class.
LaunchWorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
Constructor for LaunchWorkflowController.
LaunchWorkflowListController - Class in net.sourceforge.solexatools.webapp.controller
LaunchWorkflowListController class.
LaunchWorkflowListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController
Constructor for LaunchWorkflowListController.
LaunchWorkflowListDetailsController - Class in net.sourceforge.solexatools.webapp.controller
LaunchWorkflowListDetailsController class.
LaunchWorkflowListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
Constructor for LaunchWorkflowListDetailsController.
LaunchWorkflowSetupController - Class in net.sourceforge.solexatools.webapp.controller
LaunchWorkflowSetupController class.
LaunchWorkflowSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController
Constructor for LaunchWorkflowSetupController.
LaunchWorkflowUtil - Class in net.sourceforge.solexatools.util
LaunchWorkflowUtil class.
LaunchWorkflowUtil() - Constructor for class net.sourceforge.solexatools.util.LaunchWorkflowUtil
 
LazyFeatureSet - Class in com.github.seqware.queryengine.model.impl.lazy
An "lazy" representation of a feature set.
LazyFeatureSet() - Constructor for class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
Creates an in-memory feature set.
LazyFeatureSet.BatchedRowFeatureListsIterator - Class in com.github.seqware.queryengine.model.impl.lazy
Go through the raw iterator from the underlying storage type and batch up the FeatureLists and return them by rows
LazyFeatureSet.BatchedRowFeatureListsIterator() - Constructor for class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.BatchedRowFeatureListsIterator
 
LazyFeatureSet.Builder - Class in com.github.seqware.queryengine.model.impl.lazy
 
LazyFeatureSet.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.Builder
 
LazyFeatureSet.ConsolidatedFeatureIterator - Class in com.github.seqware.queryengine.model.impl.lazy
Iterates through Features given FeatureLists sorted by rows
LazyFeatureSet.ConsolidatedFeatureIterator() - Constructor for class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.ConsolidatedFeatureIterator
 
LazyLatestReference<T extends Atom> - Class in com.github.seqware.queryengine.util
Lazy reference class, needed if we wish to reduce the number of random accesses when deserializing objects or creating HBase specific model implementations.
LazyLatestReference(Class<T>) - Constructor for class com.github.seqware.queryengine.util.LazyLatestReference
Constructor for LazyLatestReference.
LazyMolSet<S extends MolSetInterface,T> - Interface in com.github.seqware.queryengine.model.impl
LazyMolSet interface.
LazyReference<T extends Atom> - Class in com.github.seqware.queryengine.util
Lazy reference class, needed if we wish to reduce the number of random accesses when de-serializing objects or creating HBase specific model implementations.
LazyReference(Class<T>) - Constructor for class com.github.seqware.queryengine.util.LazyReference
Constructor for LazyReference.
LEASTSIGBITS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
LibrariesResource - Class in net.sourceforge.seqware.webservice.resources.tables
LibrariesResource class.
LibrariesResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LibrariesResource
Constructor for LibrariesResource.
libraryconstructionprotocol - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
 
LibraryDAO - Interface in net.sourceforge.seqware.common.dao
LibraryDAO interface.
LibraryDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
LibraryDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate
 
librarydescriptor - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
 
LibraryDto - Class in net.sourceforge.seqware.webservice.dto
 
LibraryDto() - Constructor for class net.sourceforge.seqware.webservice.dto.LibraryDto
 
LibraryIdentityDto - Class in net.sourceforge.seqware.webservice.dto
 
LibraryIdentityDto() - Constructor for class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto
 
librarylayout - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
 
libraryname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
 
LibraryResource - Class in net.sourceforge.seqware.webservice.resources.tables
LibraryResource class.
LibraryResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LibraryResource
Constructor for LibraryResource.
LibrarySelection - Class in net.sourceforge.seqware.common.model
LibrarySelection class.
LibrarySelection() - Constructor for class net.sourceforge.seqware.common.model.LibrarySelection
Constructor for LibrarySelection.
libraryselection - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
 
LibrarySelectionDAO - Interface in net.sourceforge.seqware.common.dao
LibrarySelectionDAO interface.
LibrarySelectionDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
LibrarySelectionDAOHibernate class.
LibrarySelectionDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate
Constructor for LibrarySelectionDAOHibernate.
LibrarySelectionList - Class in net.sourceforge.seqware.common.model.lists
LibrarySelectionList class.
LibrarySelectionList() - Constructor for class net.sourceforge.seqware.common.model.lists.LibrarySelectionList
Constructor for LibrarySelectionList.
LibrarySelectionResource - Class in net.sourceforge.seqware.webservice.resources.tables
ExperimentResource class.
LibrarySelectionResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LibrarySelectionResource
Constructor for ExperimentResource.
LibrarySelectionService - Interface in net.sourceforge.seqware.common.business
LibrarySelectionService interface.
LibrarySelectionServiceImpl - Class in net.sourceforge.seqware.common.business.impl
LibrarySelectionServiceImpl class.
LibrarySelectionServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl
Constructor for LibrarySelectionServiceImpl.
LibraryService - Interface in net.sourceforge.seqware.common.business
LibraryService interface.
LibraryServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
LibraryServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl
 
LibrarySource - Class in net.sourceforge.seqware.common.model
LibrarySource class.
LibrarySource() - Constructor for class net.sourceforge.seqware.common.model.LibrarySource
Constructor for LibrarySource.
librarysource - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
 
LibrarySourceDAO - Interface in net.sourceforge.seqware.common.dao
LibrarySourceDAO interface.
LibrarySourceDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
LibrarySourceDAOHibernate class.
LibrarySourceDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate
Constructor for LibrarySourceDAOHibernate.
LibrarySourceList - Class in net.sourceforge.seqware.common.model.lists
LibrarySourceList class.
LibrarySourceList() - Constructor for class net.sourceforge.seqware.common.model.lists.LibrarySourceList
Constructor for LibrarySourceList.
LibrarySourceResource - Class in net.sourceforge.seqware.webservice.resources.tables
ExperimentResource class.
LibrarySourceResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LibrarySourceResource
Constructor for ExperimentResource.
LibrarySourceService - Interface in net.sourceforge.seqware.common.business
LibrarySourceService interface.
LibrarySourceServiceImpl - Class in net.sourceforge.seqware.common.business.impl
LibrarySourceServiceImpl class.
LibrarySourceServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl
Constructor for LibrarySourceServiceImpl.
LibraryStrategy - Class in net.sourceforge.seqware.common.model
LibraryStrategy class.
LibraryStrategy() - Constructor for class net.sourceforge.seqware.common.model.LibraryStrategy
Constructor for LibraryStrategy.
librarystrategy - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
 
LibraryStrategyDAO - Interface in net.sourceforge.seqware.common.dao
LibraryStrategyDAO interface.
LibraryStrategyDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
LibraryStrategyDAOHibernate class.
LibraryStrategyDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate
Constructor for LibraryStrategyDAOHibernate.
LibraryStrategyList - Class in net.sourceforge.seqware.common.model.lists
LibraryStrategyList class.
LibraryStrategyList() - Constructor for class net.sourceforge.seqware.common.model.lists.LibraryStrategyList
Constructor for LibraryStrategyList.
LibraryStrategyResource - Class in net.sourceforge.seqware.webservice.resources.tables
ExperimentResource class.
LibraryStrategyResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LibraryStrategyResource
Constructor for ExperimentResource.
LibraryStrategyService - Interface in net.sourceforge.seqware.common.business
LibraryStrategyService interface.
LibraryStrategyServiceImpl - Class in net.sourceforge.seqware.common.business.impl
LibraryStrategyServiceImpl class.
LibraryStrategyServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl
Constructor for LibraryStrategyServiceImpl.
linkAccessionAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
linkAccessionAndParent.
linkAccessionAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
linkAccessionAndParent.
linkProcessingAndFile(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
linkProcessingAndFile.
linkWorkflowRunAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
linkWorkflowRunAndParent.
linkWorkflowRunAndParent(int, int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
linkWorkflowRunAndParent.
linkWorkflowRunAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
linkWorkflowRunAndParent.
linkWorkflowRunAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
linkWorkflowRunAndParent.
linkWorkflowRunAndParent(WorkflowRun, int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowManager
linkWorkflowRunAndParent.
list() - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ExperimentService
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
list.
list(Study) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService
list.
list() - Method in interface net.sourceforge.seqware.common.business.FileService
list.
list() - Method in interface net.sourceforge.seqware.common.business.FileTypeService
list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl
list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
list.
list(Study) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
list.
list(Registration, String) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
list.
list(List<Integer>) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl
list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl
list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl
list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl
list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.SampleSearchServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
list.
list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
list.
list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
list.
list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
list.
list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
list.
list() - Method in interface net.sourceforge.seqware.common.business.InvoiceService
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
list.
list(Registration, String) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
list.
list() - Method in interface net.sourceforge.seqware.common.business.IUSService
list.
list(List<Integer>) - Method in interface net.sourceforge.seqware.common.business.LaneService
list.
list() - Method in interface net.sourceforge.seqware.common.business.LaneService
list.
list() - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService
list.
list() - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService
list.
list() - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService
list.
list() - Method in interface net.sourceforge.seqware.common.business.OrganismService
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.OrganismService
list.
list() - Method in interface net.sourceforge.seqware.common.business.PlatformService
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.PlatformService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ProjectService
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.ProjectService
list.
list() - Method in interface net.sourceforge.seqware.common.business.SampleSearchService
list.
list() - Method in interface net.sourceforge.seqware.common.business.SampleService
list.
list() - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
list.
list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ShareFileService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
list.
list() - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.StudyService
list.
list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService
list.
list() - Method in interface net.sourceforge.seqware.common.business.StudyService
list.
list() - Method in interface net.sourceforge.seqware.common.business.StudyTypeService
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService
list.
list() - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
list.
list() - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
list.
list() - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
list.
list() - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
list.
list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
list.
list() - Method in interface net.sourceforge.seqware.common.business.WorkflowService
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
list.
list(Study) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.FileDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.FileTypeDAO
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate
list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
list.
list(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.FileTypeDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
list.
list(Registration, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
list.
list(List<Integer>) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate
list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate
list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate
list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate
list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate
list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleSearchDAOHibernate
list.
list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate
list.
list(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate
list.
list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate
list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
list.
list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
list.
list() - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
list.
list(Registration, String) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
list.
list(List<Integer>) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.LibrarySelectionDAO
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.LibrarySelectionDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.LibrarySourceDAO
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.LibrarySourceDAO
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.LibraryStrategyDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.LibraryStrategyDAO
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.OrganismDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.OrganismDAO
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.PlatformDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.PlatformDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.SampleSearchDAO
list.
list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO
list.
list(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO
list.
list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
list.
list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
list.
list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
list.
ListBEDExporter - Class in net.sourceforge.seqware.queryengine.tools.exporters
ListBEDExporter class.
ListBEDExporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.exporters.ListBEDExporter
 
listByParentProcessingId(int) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
 
listByParentProcessingId(int) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService
 
listByParentProcessingId(int) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate
 
listByParentProcessingId(int) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO
 
listComplete() - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
listComplete.
listComplete() - Method in interface net.sourceforge.seqware.common.business.SampleService
listComplete.
listComplete() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
listComplete.
listComplete() - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
listComplete.
listFields(String) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
list the fields available to set
listFile(Registration, String, List<File>, String[], String[]) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
listFile.
listFile(Registration, String, List<File>, String[], String[]) - Method in interface net.sourceforge.seqware.common.business.LaneService
listFile.
listFilesRecursive(File, ArrayList<File>) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
listFilesRecursive.
listIncomplete() - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
listIncomplete.
listIncomplete() - Method in interface net.sourceforge.seqware.common.business.SampleService
listIncomplete.
listIncomplete() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
listIncomplete.
listIncomplete() - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
listIncomplete.
listInstalledWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
listInstalledWorkflowParams.
listInstalledWorkflowParams(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
listInstalledWorkflowParams.
listInstalledWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
listInstalledWorkflowParams.
listInstalledWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
listInstalledWorkflowParams.
listInstalledWorkflows() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
listInstalledWorkflows.
listInstalledWorkflows() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
listInstalledWorkflows.
listInstalledWorkflows() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
listInstalledWorkflows.
listInstalledWorkflows() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
listInstalledWorkflows.
listMyShared(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
listMyShared.
listMyShared(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
listMyShared.
listMyShared(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
listMyShared.
listMyShared(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
listMyShared.
listMyShared(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService
listMyShared.
listMyShared(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
listMyShared.
listMyShared(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
listMyShared.
listMyShared(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
listMyShared.
listMyShared(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
listMyShared.
listMyShared(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
listMyShared.
listMyShared(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
listMyShared.
listMyShared(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
listMyShared.
listMyShared(Registration) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
listMyShared.
listMyShared(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
listMyShared.
listRelatedWorkflows(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
listRelatedWorkflows.
listRelatedWorkflows(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
listRelatedWorkflows.
listRelatedWorkflows(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
listRelatedWorkflows.
listRelatedWorkflows(Registration) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
listRelatedWorkflows.
listRunning(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
listRunning.
listRunning(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
listRunning.
listRunning(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
listRunning.
listRunning(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
listRunning.
listRunning(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
listRunning.
listRunning(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
listRunning.
listSample(Registration) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
listSample.
listSample(Registration) - Method in interface net.sourceforge.seqware.common.business.SampleService
listSample.
listSample(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
listSample.
listSample(Registration) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
listSample.
listSequencerRunsWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
listSequencerRunsWorkflows.
listSequencerRunsWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
listSequencerRunsWorkflows.
listSharedWithMe(Registration) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
listSharedWithMe.
listSharedWithMe(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
listSharedWithMe.
listSharedWithMe(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
listSharedWithMe.
listSharedWithMe(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
listSharedWithMe.
listSharedWithMe(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
listSharedWithMe.
listSharedWithMe(Registration) - Method in interface net.sourceforge.seqware.common.business.StudyService
listSharedWithMe.
listSharedWithMe(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService
listSharedWithMe.
listSharedWithMe(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
listSharedWithMe.
listSharedWithMe(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
listSharedWithMe.
listSharedWithMe(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
listSharedWithMe.
listSharedWithMe(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
listSharedWithMe.
listSharedWithMe(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
listSharedWithMe.
listSharedWithMe(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
listSharedWithMe.
listSharedWithMe(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
listSharedWithMe.
listSharedWithMe(Registration) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
listSharedWithMe.
listSharedWithMe(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
listSharedWithMe.
listSharedWithMeWithSample(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
listSharedWithMeWithSample.
listSharedWithMeWithSample(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
listSharedWithMeWithSample.
listStudyHasFile(Registration, String, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
listStudyHasFile.
listStudyHasFile(Registration, String, Boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService
listStudyHasFile.
listStudyHasFile(Registration, String, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
listStudyHasFile.
listStudyHasFile(Registration, String, Boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
listStudyHasFile.
listWithHasFile(SortedSet<Experiment>, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
listWithHasFile.
listWithHasFile(SortedSet<Experiment>, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
listWithHasFile.
listWithHasFile(SortedSet<IUS>, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
listWithHasFile.
listWithHasFile(SortedSet<Lane>, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
listWithHasFile.
listWithHasFile(Integer, SortedSet<Sample>, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
listWithHasFile.
listWithHasFile(List<Study>) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
listWithHasFile.
listWithHasFile(List<Study>, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
listWithHasFile.
listWithHasFile(List<WorkflowRun>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
listWithHasFile.
listWithHasFile(SortedSet<IUS>, String) - Method in interface net.sourceforge.seqware.common.business.IUSService
listWithHasFile.
listWithHasFile(SortedSet<Lane>, String) - Method in interface net.sourceforge.seqware.common.business.LaneService
listWithHasFile.
listWithHasFile(Integer, SortedSet<Sample>, String) - Method in interface net.sourceforge.seqware.common.business.SampleService
listWithHasFile.
listWithHasFile(List<Study>) - Method in interface net.sourceforge.seqware.common.business.StudyService
listWithHasFile.
listWithHasFile(List<Study>, String) - Method in interface net.sourceforge.seqware.common.business.StudyService
listWithHasFile.
listWithHasFile(List<WorkflowRun>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
listWithHasFile.
listWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
listWorkflows.
listWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
listWorkflows.
literal() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
literal.
LiveTagResource - Class in net.sourceforge.seqware.queryengine.webservice.view
LiveTagResource class.
LiveTagResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.LiveTagResource
 
LoadIndexPageController - Class in net.sourceforge.solexatools.webapp.controller
LoadIndexPageController class.
LoadIndexPageController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController
Constructor for LoadIndexPageController.
LocatableModel - Class in net.sourceforge.seqware.queryengine.backend.model
LocatableModel class.
LocatableModel() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
 
LocatableSecondaryCursorIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators
LocatableSecondaryCursorIterator class.
LocatableSecondaryCursorIterator(SecondaryCursor, DatabaseEntry, TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.LocatableSecondaryCursorIterator
Constructor for LocatableSecondaryCursorIterator.
LocatableSecondaryCursorIterator(SecondaryCursor, DatabaseEntry, ContigPosition, TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.LocatableSecondaryCursorIterator
Constructor for LocatableSecondaryCursorIterator.
locateFile(String) - Method in class net.sourceforge.seqware.common.metadata.Metadata
locateFile.
lockAndAppend(File, String) - Static method in class net.sourceforge.seqware.common.util.filetools.lock.LockingFileTools
Try to acquire lock.
lockAndAppendLine(File, String) - Static method in class net.sourceforge.seqware.common.util.filetools.lock.LockingFileTools
lockAndAppendLine.
LockingFileTools - Class in net.sourceforge.seqware.common.util.filetools.lock
LockingFileTools class.
LockingFileTools() - Constructor for class net.sourceforge.seqware.common.util.filetools.lock.LockingFileTools
 
Log - Class in net.sourceforge.seqware.common.util
Log class.
LOG - Static variable in interface net.sourceforge.seqware.pipeline.runner.RunnerParams.Bean
 
log(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareBase
log.
log(String) - Static method in class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROC
log.
log(String) - Static method in class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROCHBase
log.
LogAspect - Class in net.sourceforge.seqware.pipeline.runner
This is a test class Created by IntelliJ IDEA.
LogAspect() - Constructor for class net.sourceforge.seqware.pipeline.runner.LogAspect
 
logging() - Method in class net.sourceforge.seqware.pipeline.runner.DefaultConfig
logging.
LoginController - Class in net.sourceforge.solexatools.webapp.controller
LoginController
LoginController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LoginController
Constructor for LoginController.
loginSuccess(String, String) - Method in class net.sourceforge.solexatools.authentication.Authentication
loginSuccess.
loginSuccess(String, String) - Method in class net.sourceforge.solexatools.authentication.OICRLdapAuthentication
loginSuccess.
loginSuccess(String, String) - Method in class net.sourceforge.solexatools.authentication.UNCKerberos
loginSuccess.
LoginValidator - Class in net.sourceforge.solexatools.validation
LoginValidator class.
LoginValidator() - Constructor for class net.sourceforge.solexatools.validation.LoginValidator
Constructor for LoginValidator.
LogoutController - Class in net.sourceforge.solexatools.webapp.controller
LogoutController class.
LogoutController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LogoutController
Constructor for LogoutController.
low_precedence_constraint() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
low_precedence_constraint.
LowLevelBackEndInterface - Interface in com.github.seqware.queryengine.backInterfaces
This interface specifies operations to persist, update, and add objects to the back-end without knowing about the specific database back-end.
ls454 - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
 
LT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant LT=15
LT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant LT=15
LTEQ - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant LTEQ=16
LTEQ - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant LTEQ=16

M

m2pb(Feature) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureIO
Convert from model to protein buffer object
m2pb(FeatureList) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureListIO
Convert from model to protein buffer object
m2pb(FeatureSet) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureSetIO
Convert from model to protein buffer object
m2pb(FSGID) - Static method in class com.github.seqware.queryengine.impl.protobufIO.FSGIDIO
m2pb.
m2pb(Group) - Method in class com.github.seqware.queryengine.impl.protobufIO.GroupIO
Convert from model to protein buffer object
m2pb(Plugin) - Method in class com.github.seqware.queryengine.impl.protobufIO.PluginIO
Convert from model to protein buffer object
m2pb(PluginRun) - Method in class com.github.seqware.queryengine.impl.protobufIO.PluginRunIO
Convert from model to protein buffer object
m2pb(T) - Method in interface com.github.seqware.queryengine.impl.protobufIO.ProtobufTransferInterface
Convert from model to protein buffer object
m2pb(Reference) - Method in class com.github.seqware.queryengine.impl.protobufIO.ReferenceIO
Convert from model to protein buffer object
m2pb(ReferenceSet) - Method in class com.github.seqware.queryengine.impl.protobufIO.ReferenceSetIO
Convert from model to protein buffer object
m2pb(SGID) - Static method in class com.github.seqware.queryengine.impl.protobufIO.SGIDIO
m2pb.
m2pb(Tag) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagIO
Convert from model to protein buffer object
m2pb(TagSet) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagSetIO
Convert from model to protein buffer object
m2pb(Tag) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagSpecIO
Convert from model to protein buffer object
m2pb(User) - Method in class com.github.seqware.queryengine.impl.protobufIO.UserIO
Convert from model to protein buffer object
main(String[]) - Static method in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper
Command-line interface
main(String[]) - Static method in class com.github.seqware.queryengine.system.exporters.VCFDumper
main.
main(String[]) - Static method in class com.github.seqware.queryengine.system.importers.FeatureImporter
main.
main(String[]) - Static method in class com.github.seqware.queryengine.system.importers.OBOImporter
main.
main(String[]) - Static method in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
Command-line interface
main(String[]) - Static method in class com.github.seqware.queryengine.system.ReferenceCreator
main.
main(String[]) - Static method in class com.github.seqware.queryengine.system.rest.QueryEngineService
 
main(String[]) - Static method in class com.github.seqware.queryengine.system.TagSetCreator
main.
main(String[]) - Static method in class com.github.seqware.queryengine.tutorial.BrianTest
main.
main(String[]) - Static method in class com.github.seqware.queryengine.tutorial.GITest
main.
main(String[]) - Static method in class com.github.seqware.queryengine.tutorial.Poster
main.
main(String[]) - Static method in class com.github.seqware.queryengine.tutorial.PosterSGE
main.
main(String[]) - Static method in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
main.
main(String[]) - Static method in class net.sourceforge.seqware.common.metadata.ProcessingTaskGroup.ProcessingTaskGroup
main.
main(String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
main.
main(String[]) - Static method in class net.sourceforge.seqware.common.util.TabExpansionUtil
 
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.daxgenerator.Daxgenerator
main.
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.module.TestModule
main.
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
 
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.runner.PluginRunner
main.
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner
main.
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner2
main.
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.tools.ReportTest
main.
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.tools.UnZip
main.
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.tools.Zip
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROC
A simple program that takes a list of posit
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROCHBase
A simple program that takes a list of posit
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROCOld
A simple program that takes a list of posit
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.BlobReaderWriter
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.HBaseRead2
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.ImporterTest
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.ImporterTest2
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.MapReduceTest
Main entry point.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.MapReduceTest2
Main entry point.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.annotators.AnnotateVariantsWithContigAndZygosity
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.exporters.BEDExporter
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.exporters.ListBEDExporter
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.exporters.TagDumper
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.exporters.TextDumper
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.exporters.WIGExporter
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.FeatureImporter
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.PileupCoverageImporter
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.TagAnnotationByPositionImporter
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.TagAnnotationImporter
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.VariantConsequenceByPositionImporter
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.VariantConsequenceImporter
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.VariantImporter
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.iterators.CoverageIteratorProcessor
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.iterators.VariantIteratorProcessor
main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.reporters.CompareTwoVariantAndCoverageDatabases
A simple program that takes a list of posit
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.reporters.CompareTwoVariantDatabases
FIXME: add param to pass in range to compare over eg chr22 or chr1:123-1231231
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceMain
main.
mainMethod(String[]) - Static method in class com.github.seqware.queryengine.system.importers.OBOImporter
Import a set of Tag specifications into a new TagSet.
mainMethod(String[]) - Static method in class com.github.seqware.queryengine.system.ReferenceCreator
Create a reference given just a name for the new reference to be created.
mainMethod(String[]) - Static method in class com.github.seqware.queryengine.system.TagSetCreator
Create a reference given just a name for the new reference to be created.
makeReport(String) - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport
makeReport.
manageFlushedObjects(List<Map.Entry<String, SimpleModelManager.AtomStatePair>>) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
manageFlushedObjects.
ManageWorkflowsController - Class in net.sourceforge.solexatools.webapp.controller
ManageWorkflowsController class.
ManageWorkflowsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController
Constructor for ManageWorkflowsController.
mAND() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mAND.
manipulateRPNStack(RPNStack, Feature, List<TagSet>, Map<String, Tag>) - Static method in class com.github.seqware.queryengine.plugins.plugins.FeaturesByAttributesPlugin.FeaturesByAttributesFilter
 
map(ImmutableBytesWritable, Result, Mapper.Context) - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner.PluginRunnerMapper
 
map(Collection<Feature>, MapperInterface<MAPKEYOUT, MAPVALUEOUT>) - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
Mapping implementation that singles out desired atoms into a mapped set.
map(Collection<Feature>, MapperInterface<Collection<Feature>, FeatureSet>) - Method in class com.github.seqware.queryengine.plugins.plugins.FeaturesByFilterPlugin
Mapping implementation that singles out desired atoms into a mapped set.
map(Collection<Feature>, MapperInterface<Collection<Feature>, Object>) - Method in class com.github.seqware.queryengine.plugins.plugins.FeatureSetCountPlugin
 
map(Collection<Feature>, MapperInterface<Text, Text>) - Method in class com.github.seqware.queryengine.plugins.plugins.VCFDumperPlugin
 
mapCleanup() - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
mapperCleanup.
mapCleanup() - Method in class com.github.seqware.queryengine.plugins.plugins.FeaturesByFilterPlugin
 
mapExpandVariables(Map) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools
mapExpandVariables.
mapInit(MapperInterface) - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
mapInit.
mapInit(MapperInterface) - Method in class com.github.seqware.queryengine.plugins.plugins.FeaturesByFilterPlugin
 
MapperInterface<KEYOUT,VALUEOUT> - Interface in com.github.seqware.queryengine.plugins
 
MapperInterface.Counters - Enum in com.github.seqware.queryengine.plugins
Counter enumeration to count the actual rows.
mapProcessingIdToAccession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
mapProcessingIdToAccession.
mapProcessingIdToAccession(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
mapProcessingIdToAccession.
mapProcessingIdToAccession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
mapProcessingIdToAccession.
mapProcessingIdToAccession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
mapProcessingIdToAccession.
MapReducePlugin<MAPKEYOUT,MAPVALUEOUT,REDUCEKEYIN,REDUCEVALUEIN,REDUCEKEYOUT,REDUCEVALUEOUT,RESULT> - Class in com.github.seqware.queryengine.plugins
An abstracted map-reduce interface.
MapReducePlugin() - Constructor for class com.github.seqware.queryengine.plugins.MapReducePlugin
 
MapReduceTest - Class in net.sourceforge.seqware.queryengine.prototypes.hadoop
TODO: > iterate over each row and pull out variant objects > check to see if both variants exists at position > if they do then increment counter > write the counter to an hdfs file > need to figure out how to pass parameters to map and reduce classes!
MapReduceTest() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.hadoop.MapReduceTest
 
MapReduceTest2 - Class in net.sourceforge.seqware.queryengine.prototypes.hadoop
TODO: > iterate over each row and pull out variant objects > check to see if both variants exists at position > if they do then increment counter > write the counter to an hdfs file > need to figure out how to pass parameters to map and reduce classes!
MapReduceTest2() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.hadoop.MapReduceTest2
 
mapString2Int(Map) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools
mapString2Int.
MapTools - Class in net.sourceforge.seqware.common.util.maptools
MapTools class.
MapTools() - Constructor for class net.sourceforge.seqware.common.util.maptools.MapTools
 
markDatabaseChanged() - Static method in class net.sourceforge.seqware.common.util.testtools.DatabaseCreator
markDatabaseChanged.
markDatabaseChanged() - Static method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator
markDatabaseChanged.
MarkdownPlugin - Class in net.sourceforge.seqware.pipeline.plugins
This plugin outputs documentation for our plugins and modules in markdown format
MarkdownPlugin() - Constructor for class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
Constructor for HelloWorld.
MarkdownPlugin.MarkDownFormatter - Class in net.sourceforge.seqware.pipeline.plugins
 
MarkdownPlugin.MarkDownFormatter() - Constructor for class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin.MarkDownFormatter
 
MarkdownPlugin.ModuleComparator - Class in net.sourceforge.seqware.pipeline.plugins
 
MarkdownPlugin.ModuleComparator() - Constructor for class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin.ModuleComparator
 
MarkdownPlugin.PluginComparator - Class in net.sourceforge.seqware.pipeline.plugins
 
MarkdownPlugin.PluginComparator() - Constructor for class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin.PluginComparator
 
marshal(Set<File>) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeFileSet
marshal(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeIUSSortedSet
marshal(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeLaneSortedSet
marshal(String) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeXML
marshal(T) - Method in class net.sourceforge.seqware.common.util.xmltools.JaxbObject
Turn an object into XML using JAXB and provide the result in a StreamResult.
marshalToDocument(T) - Method in class net.sourceforge.seqware.common.util.xmltools.JaxbObject
Turn an object into XML using JAXB and provide the result in a StreamResult.
marshalToDocument(JaxbObject, Object) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools
marshalToDocument.
matchName(String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
 
matchName(String) - Method in interface net.sourceforge.seqware.common.business.SampleService
 
matchName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
findByName.
matchName(String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
findByName.
MAX_BASE - Static variable in class com.github.seqware.queryengine.kernel.Compression
Constant MAX_BASE=94
maxCoverage - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
maximumMappingQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
maxThreads - Variable in class com.github.seqware.queryengine.system.importers.Importer
 
maxThreads - Variable in class net.sourceforge.seqware.queryengine.tools.importers.Importer
 
maxThreads - Static variable in class net.sourceforge.seqware.queryengine.webservice.model.BackendPool
Constant maxThreads=Integer.parseInt(EnvUtil.getProperty("maxconnections"))
MAXVERSIONS - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
Constant MAXVERSIONS=1000
mBRACKET_CLOSE() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mBRACKET_CLOSE.
mBRACKET_OPEN() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mBRACKET_OPEN.
mCOMMENT_EOL() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mCOMMENT_EOL.
mCOMMENT_INLINE() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mCOMMENT_INLINE.
MD5Generator - Class in net.sourceforge.seqware.common.util
Utility class for calculating MD5 hash on a file's contents.
MD5Generator() - Constructor for class net.sourceforge.seqware.common.util.MD5Generator
 
md5sum(String) - Method in class net.sourceforge.seqware.common.util.MD5Generator
Returns a 32 character representation of the MD5 hash of the specified file's content.
md5sumFile(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
md5sumFile.
member - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF
 
member - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS
 
members - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
 
mEQUALS() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mEQUALS.
merge(Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
merge.
merge(Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
merge.
merge(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
merge.
merge(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
merge.
merge(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
merge.
merge(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
merge.
merge(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
merge.
merge(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
merge.
merge(String, String, Map) - Static method in class net.sourceforge.seqware.common.util.freemarker.Freemarker
merge.
mergeAcl(QueryEngine.ACLPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
mergeAtom(QESupporting.FeatureAtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
mergeFeatureSet(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
mergeFrom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
mergeFrom(QESupporting.FeatureAtomPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
mergeFrom(QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
mergeFrom(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
mergeFrom(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
mergeFrom(QueryEngine.ACLPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
mergeFrom(QueryEngine.FeatureListPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
mergeFrom(QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
mergeFrom(QueryEngine.FeatureSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
mergeFrom(QueryEngine.GroupPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
mergeFrom(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
mergeFrom(QueryEngine.PluginPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
mergeFrom(QueryEngine.PluginRunPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
mergeFrom(QueryEngine.ReferencePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
mergeFrom(QueryEngine.ReferenceSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
mergeFrom(QueryEngine.TagSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
mergeFrom(QueryEngine.UserPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
mergeGrp(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
mergePrecedingID(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
mergePrecedingID(QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
mergePrecedingVersion(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
mergePrecedingVersion(QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
mergePrecedingVersion(QueryEngine.FeatureSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
mergePrecedingVersion(QueryEngine.GroupPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
mergePrecedingVersion(QueryEngine.PluginPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
mergePrecedingVersion(QueryEngine.PluginRunPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
mergePrecedingVersion(QueryEngine.ReferencePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
mergePrecedingVersion(QueryEngine.ReferenceSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
mergePrecedingVersion(QueryEngine.TagSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
mergePrecedingVersion(QueryEngine.UserPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
mergeReferenceID(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
mergeSgid(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
mergeSgid(QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
mergeSgid(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
mergeTagSet(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
mergeUser(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
mergeVSGIDRef(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
Metadata - Class in net.sourceforge.seqware.common.metadata
Abstract Metadata class.
Metadata() - Constructor for class net.sourceforge.seqware.common.metadata.Metadata
 
metadata - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
metadata - Variable in class net.sourceforge.seqware.pipeline.decider.Decider
 
metadata - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
Metadata - Class in net.sourceforge.seqware.pipeline.plugins
This plugin currently lets users creation a limited set of table rows in the database from the command line.
Metadata() - Constructor for class net.sourceforge.seqware.pipeline.plugins.Metadata
Constructor for Metadata.
metadata - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
MetadataDB - Class in net.sourceforge.seqware.common.metadata
MetadataDB class.
MetadataDB() - Constructor for class net.sourceforge.seqware.common.metadata.MetadataDB
Constructor for MetadataDB.
MetadataDB - Class in net.sourceforge.seqware.queryengine.webservice.model
MetadataDB class.
MetadataDB() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
 
MetadataInterface - Interface in net.sourceforge.seqware.common.metadata
MetadataInterface interface.
METADATAINVALIDIDCHAIN - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant METADATAINVALIDIDCHAIN=8
MetadataNoConnection - Class in net.sourceforge.seqware.common.metadata
MetadataNoConnection class.
MetadataNoConnection() - Constructor for class net.sourceforge.seqware.common.metadata.MetadataNoConnection
 
metadataWriteback - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
MetadataWS - Class in net.sourceforge.seqware.common.metadata
TODO: this needs to setup rows in experiment_library_design and experiment_spot_design
MetadataWS() - Constructor for class net.sourceforge.seqware.common.metadata.MetadataWS
Constructor for MetadataWS.
MetadataWS.LowLevel - Class in net.sourceforge.seqware.common.metadata
 
MetadataWS.LowLevel(String, String, String) - Constructor for class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
 
metaMap - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
mFLOAT() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mFLOAT.
mGT() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mGT.
mGTEQ() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mGTEQ.
mID() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mID.
minCoverage - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
minSnpQuality - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
mINT() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mINT.
MINUS_STRAND - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Constant MINUS_STRAND=2
mismatchAAChangeBlosumScore - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
mismatchAminoAcidChange - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
mismatchChr - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
mismatchCodonChange - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
mismatchCodonPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
MismatchConsequenceReportProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators.processors
MismatchConsequenceReportProcessor class.
MismatchConsequenceReportProcessor(String, Store, boolean, boolean, int, int, int, int, int, int) - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.MismatchConsequenceReportProcessor
Constructor for MismatchConsequenceReportProcessor.
MismatchConsequenceReportProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.MismatchConsequenceReportProcessor
Constructor for MismatchConsequenceReportProcessor.
MismatchesResource - Class in net.sourceforge.seqware.queryengine.webservice.view
MismatchesResource class.
MismatchesResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.MismatchesResource
 
mismatchId - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
MismatchResource - Class in net.sourceforge.seqware.queryengine.webservice.view
MismatchResource class.
MismatchResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.MismatchResource
 
mismatchStart - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
mismatchStop - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
mismatchType - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
mLT() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mLT.
mLTEQ() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mLTEQ.
mNAMED_CONSTANT() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mNAMED_CONSTANT.
mNAMED_FUNCTION() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mNAMED_FUNCTION.
mNAMED_THREE_PARAM_PREDICATE() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mNAMED_THREE_PARAM_PREDICATE.
mNAMED_TWO_PARAM_PREDICATE() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mNAMED_TWO_PARAM_PREDICATE.
mNOT() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mNOT.
mNOTEQUALS() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mNOTEQUALS.
Model - Class in net.sourceforge.seqware.queryengine.backend.model
Model class.
Model() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.Model
 
ModelInterface - Interface in net.sourceforge.seqware.queryengine.backend.model
ModelInterface interface.
ModelUtil - Class in net.sourceforge.solexatools.util
ModelUtil class.
ModelUtil() - Constructor for class net.sourceforge.solexatools.util.ModelUtil
 
modify - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
 
modifyIniFile(String, String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
Module - Class in net.sourceforge.seqware.pipeline.module
Abstract Module class.
Module() - Constructor for class net.sourceforge.seqware.pipeline.module.Module
 
MODULE - Static variable in interface net.sourceforge.seqware.pipeline.runner.RunnerParams.Bean
 
Module - Enum in net.sourceforge.seqware.pipeline.workflowV2.model
Module class.
ModuleInterface - Interface in net.sourceforge.seqware.pipeline.module
This interface defines the required behavior of a SeqWare module.
ModuleMethod - Enum in net.sourceforge.seqware.pipeline.module
Enumeration class for ModuleMethod Created by IntelliJ IDEA.
ModuleRunner - Class in net.sourceforge.seqware.pipeline.plugins
ModuleRunner class.
ModuleRunner() - Constructor for class net.sourceforge.seqware.pipeline.plugins.ModuleRunner
Constructor for ModuleRunner.
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
Molecule<T extends Molecule> - Interface in com.github.seqware.queryengine.model
Defines core functionality that is shared by classes that are controlled by permissions and are atoms
MoleculeImpl<T extends Molecule> - Class in com.github.seqware.queryengine.model.impl
Implements core functionality that is shared by classes that are controlled by permissions and Versionable, Taggable, TTLable via AtomImpl)
MoleculeImpl() - Constructor for class com.github.seqware.queryengine.model.impl.MoleculeImpl
 
MolSetInterface<S extends MolSetInterface,T> - Interface in com.github.seqware.queryengine.model.interfaces
Abstracts out some of the semantics for interacting with each of our Set classes.
mOR() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mOR.
MOSTSIGBITS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
MRHBaseModelManager - Class in com.github.seqware.queryengine.impl
A Simple implementation of the CreateUpdateManager interface.
MRHBaseModelManager() - Constructor for class com.github.seqware.queryengine.impl.MRHBaseModelManager
 
MRHBasePersistentBackEnd - Class in com.github.seqware.queryengine.impl
Implement HBase optimizations for the back-end.
MRHBasePersistentBackEnd(StorageInterface) - Constructor for class com.github.seqware.queryengine.impl.MRHBasePersistentBackEnd
Constructor for MRHBasePersistentBackEnd.
MRHBasePluginRunner<ReturnType> - Class in com.github.seqware.queryengine.plugins.hbasemr
Abstract implementation of an abstract map/reduce-based plug-in runner for a HBase back-end.
MRHBasePluginRunner(MapReducePlugin, FeatureSet, Object...) - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner
 
MRHBasePluginRunner.PluginRunnerMapper<KEYOUT,VALUEOUT> - Class in com.github.seqware.queryengine.plugins.hbasemr
 
MRHBasePluginRunner.PluginRunnerMapper() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner.PluginRunnerMapper
 
MRHBasePluginRunner.PluginRunnerReducer<KEYIN,VALUEIN,KEYOUT,VALUEOUT> - Class in com.github.seqware.queryengine.plugins.hbasemr
 
MRHBasePluginRunner.PluginRunnerReducer() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner.PluginRunnerReducer
 
MRLazyFeatureSet - Class in com.github.seqware.queryengine.model.impl.hbasemrlazy
An "lazy" representation of a feature set.
MRLazyFeatureSet() - Constructor for class com.github.seqware.queryengine.model.impl.hbasemrlazy.MRLazyFeatureSet
Creates an lazy M/R using feature set.
MRLazyFeatureSet.Builder - Class in com.github.seqware.queryengine.model.impl.hbasemrlazy
 
MRLazyFeatureSet.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.hbasemrlazy.MRLazyFeatureSet.Builder
 
mSTRING() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mSTRING.
mT__26() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mT__26.
mTokens() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mTokens.
multiplier - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
 
mutatedGenomicSequence - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
mutatedTranslatedSequence - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
mWHITESPACE() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
mWHITESPACE.

N

naiveRun(String[]) - Static method in class com.github.seqware.queryengine.system.importers.FeatureImporter
Import a set of Features into a particular specified reference.
NAME - Static variable in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
Constant NAME="ExperimentLibraryDesignService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.ExperimentService
Constant NAME="ExperimentService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
Constant NAME="ExperimentSpotDesignReadSpecService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService
Constant NAME="ExperimentSpotDesignService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.FileService
Constant NAME="fileService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.FileTypeService
Constant NAME="FileTypeService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.FileUploadService
Constant NAME="FileUploadService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.InvoiceService
Constant NAME="invoiceService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.IUSService
Constant NAME="IUSService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.LaneService
Constant NAME="laneService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.LibrarySelectionService
Constant NAME="LibrarySelectionService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.LibrarySourceService
Constant NAME="LibrarySourceService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.LibraryStrategyService
Constant NAME="LibraryStrategyService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.OrganismService
Constant NAME="OrganismService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.PlatformService
Constant NAME="PlatformService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.ProcessingService
Constant NAME="processingService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.ProjectService
Constant NAME="projectService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.RegistrationService
Constant NAME="registrationService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.SampleService
Constant NAME="sampleService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.SequencerRunService
Constant NAME="SequencerRunService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.ShareStudyService
Constant NAME="shareStudyService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
Constant NAME="shareWorkflowRunService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.StudyService
Constant NAME="StudyService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.StudyTypeService
Constant NAME="StudyTypeService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowParamService
Constant NAME="workflowParamService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
Constant NAME="WorkflowParamValueService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
Constant NAME="WorkflowRunParamService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowRunService
Constant NAME="WorkflowRunService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowService
Constant NAME="WorkflowService"
name - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
name - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
name - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
 
name - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
 
NAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
NAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
NAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
NAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
NAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
NAMED_CONSTANT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant NAMED_CONSTANT=17
NAMED_CONSTANT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant NAMED_CONSTANT=17
NAMED_FUNCTION - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant NAMED_FUNCTION=18
NAMED_FUNCTION - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant NAMED_FUNCTION=18
NAMED_THREE_PARAM_PREDICATE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant NAMED_THREE_PARAM_PREDICATE=19
NAMED_THREE_PARAM_PREDICATE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant NAMED_THREE_PARAM_PREDICATE=19
NAMED_TWO_PARAM_PREDICATE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant NAMED_TWO_PARAM_PREDICATE=20
NAMED_TWO_PARAM_PREDICATE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant NAMED_TWO_PARAM_PREDICATE=20
NAMESPACE - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp
 
NAMESPACE - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Adag
 
NEGATIVE_VALUE - Static variable in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
nested_constraint() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
nested_constraint.
net.sourceforge.seqware.common - package net.sourceforge.seqware.common
 
net.sourceforge.seqware.common.business - package net.sourceforge.seqware.common.business
 
net.sourceforge.seqware.common.business.impl - package net.sourceforge.seqware.common.business.impl
 
net.sourceforge.seqware.common.dao - package net.sourceforge.seqware.common.dao
 
net.sourceforge.seqware.common.dao.hibernate - package net.sourceforge.seqware.common.dao.hibernate
 
net.sourceforge.seqware.common.err - package net.sourceforge.seqware.common.err
 
net.sourceforge.seqware.common.factory - package net.sourceforge.seqware.common.factory
 
net.sourceforge.seqware.common.hibernate - package net.sourceforge.seqware.common.hibernate
 
net.sourceforge.seqware.common.hibernate.reports - package net.sourceforge.seqware.common.hibernate.reports
 
net.sourceforge.seqware.common.invitation - package net.sourceforge.seqware.common.invitation
 
net.sourceforge.seqware.common.metadata - package net.sourceforge.seqware.common.metadata
 
net.sourceforge.seqware.common.metadata.ProcessingTaskGroup - package net.sourceforge.seqware.common.metadata.ProcessingTaskGroup
 
net.sourceforge.seqware.common.model - package net.sourceforge.seqware.common.model
 
net.sourceforge.seqware.common.model.adapters - package net.sourceforge.seqware.common.model.adapters
 
net.sourceforge.seqware.common.model.comparator - package net.sourceforge.seqware.common.model.comparator
 
net.sourceforge.seqware.common.model.lists - package net.sourceforge.seqware.common.model.lists
 
net.sourceforge.seqware.common.module - package net.sourceforge.seqware.common.module
 
net.sourceforge.seqware.common.security - package net.sourceforge.seqware.common.security
 
net.sourceforge.seqware.common.util - package net.sourceforge.seqware.common.util
 
net.sourceforge.seqware.common.util.configtools - package net.sourceforge.seqware.common.util.configtools
 
net.sourceforge.seqware.common.util.exceptiontools - package net.sourceforge.seqware.common.util.exceptiontools
 
net.sourceforge.seqware.common.util.filetools - package net.sourceforge.seqware.common.util.filetools
 
net.sourceforge.seqware.common.util.filetools.lock - package net.sourceforge.seqware.common.util.filetools.lock
 
net.sourceforge.seqware.common.util.filetools.validate - package net.sourceforge.seqware.common.util.filetools.validate
 
net.sourceforge.seqware.common.util.freemarker - package net.sourceforge.seqware.common.util.freemarker
 
net.sourceforge.seqware.common.util.iotools - package net.sourceforge.seqware.common.util.iotools
 
net.sourceforge.seqware.common.util.jsontools - package net.sourceforge.seqware.common.util.jsontools
 
net.sourceforge.seqware.common.util.maptools - package net.sourceforge.seqware.common.util.maptools
 
net.sourceforge.seqware.common.util.processtools - package net.sourceforge.seqware.common.util.processtools
 
net.sourceforge.seqware.common.util.processtools.stderr - package net.sourceforge.seqware.common.util.processtools.stderr
 
net.sourceforge.seqware.common.util.processtools.stdout - package net.sourceforge.seqware.common.util.processtools.stdout
 
net.sourceforge.seqware.common.util.runtools - package net.sourceforge.seqware.common.util.runtools
 
net.sourceforge.seqware.common.util.testtools - package net.sourceforge.seqware.common.util.testtools
 
net.sourceforge.seqware.common.util.workflowtools - package net.sourceforge.seqware.common.util.workflowtools
 
net.sourceforge.seqware.common.util.xmltools - package net.sourceforge.seqware.common.util.xmltools
 
net.sourceforge.seqware.metadb.util - package net.sourceforge.seqware.metadb.util
 
net.sourceforge.seqware.pipeline.bundle - package net.sourceforge.seqware.pipeline.bundle
 
net.sourceforge.seqware.pipeline.daxgenerator - package net.sourceforge.seqware.pipeline.daxgenerator
 
net.sourceforge.seqware.pipeline.decider - package net.sourceforge.seqware.pipeline.decider
 
net.sourceforge.seqware.pipeline.deciders - package net.sourceforge.seqware.pipeline.deciders
 
net.sourceforge.seqware.pipeline.module - package net.sourceforge.seqware.pipeline.module
This package provides the SeqWare module interface and API, including common code and classes.
net.sourceforge.seqware.pipeline.module.ann - package net.sourceforge.seqware.pipeline.module.ann
 
net.sourceforge.seqware.pipeline.modules - package net.sourceforge.seqware.pipeline.modules
 
net.sourceforge.seqware.pipeline.modules.utilities - package net.sourceforge.seqware.pipeline.modules.utilities
 
net.sourceforge.seqware.pipeline.plugin - package net.sourceforge.seqware.pipeline.plugin
 
net.sourceforge.seqware.pipeline.plugins - package net.sourceforge.seqware.pipeline.plugins
 
net.sourceforge.seqware.pipeline.plugins.filelinker - package net.sourceforge.seqware.pipeline.plugins.filelinker
 
net.sourceforge.seqware.pipeline.runner - package net.sourceforge.seqware.pipeline.runner
 
net.sourceforge.seqware.pipeline.tools - package net.sourceforge.seqware.pipeline.tools
 
net.sourceforge.seqware.pipeline.workflow - package net.sourceforge.seqware.pipeline.workflow
 
net.sourceforge.seqware.pipeline.workflowV2 - package net.sourceforge.seqware.pipeline.workflowV2
 
net.sourceforge.seqware.pipeline.workflowV2.engine.oozie - package net.sourceforge.seqware.pipeline.workflowV2.engine.oozie
 
net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object - package net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object
 
net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus - package net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus
 
net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object - package net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object
 
net.sourceforge.seqware.pipeline.workflowV2.model - package net.sourceforge.seqware.pipeline.workflowV2.model
 
net.sourceforge.seqware.queryengine.backend.factory - package net.sourceforge.seqware.queryengine.backend.factory
 
net.sourceforge.seqware.queryengine.backend.factory.impl - package net.sourceforge.seqware.queryengine.backend.factory.impl
 
net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators - package net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators
 
net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators - package net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators
 
net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders - package net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders
 
net.sourceforge.seqware.queryengine.backend.model - package net.sourceforge.seqware.queryengine.backend.model
 
net.sourceforge.seqware.queryengine.backend.store - package net.sourceforge.seqware.queryengine.backend.store
 
net.sourceforge.seqware.queryengine.backend.store.impl - package net.sourceforge.seqware.queryengine.backend.store.impl
 
net.sourceforge.seqware.queryengine.backend.util - package net.sourceforge.seqware.queryengine.backend.util
 
net.sourceforge.seqware.queryengine.backend.util.iterators - package net.sourceforge.seqware.queryengine.backend.util.iterators
 
net.sourceforge.seqware.queryengine.examples - package net.sourceforge.seqware.queryengine.examples
 
net.sourceforge.seqware.queryengine.prototypes - package net.sourceforge.seqware.queryengine.prototypes
 
net.sourceforge.seqware.queryengine.prototypes.hadoop - package net.sourceforge.seqware.queryengine.prototypes.hadoop
 
net.sourceforge.seqware.queryengine.tools.annotators - package net.sourceforge.seqware.queryengine.tools.annotators
 
net.sourceforge.seqware.queryengine.tools.exporters - package net.sourceforge.seqware.queryengine.tools.exporters
 
net.sourceforge.seqware.queryengine.tools.importers - package net.sourceforge.seqware.queryengine.tools.importers
 
net.sourceforge.seqware.queryengine.tools.importers.workers - package net.sourceforge.seqware.queryengine.tools.importers.workers
 
net.sourceforge.seqware.queryengine.tools.iterators - package net.sourceforge.seqware.queryengine.tools.iterators
 
net.sourceforge.seqware.queryengine.tools.iterators.processors - package net.sourceforge.seqware.queryengine.tools.iterators.processors
 
net.sourceforge.seqware.queryengine.tools.reporters - package net.sourceforge.seqware.queryengine.tools.reporters
 
net.sourceforge.seqware.queryengine.webservice.controller - package net.sourceforge.seqware.queryengine.webservice.controller
 
net.sourceforge.seqware.queryengine.webservice.model - package net.sourceforge.seqware.queryengine.webservice.model
 
net.sourceforge.seqware.queryengine.webservice.security - package net.sourceforge.seqware.queryengine.webservice.security
 
net.sourceforge.seqware.queryengine.webservice.util - package net.sourceforge.seqware.queryengine.webservice.util
 
net.sourceforge.seqware.queryengine.webservice.view - package net.sourceforge.seqware.queryengine.webservice.view
 
net.sourceforge.seqware.webservice.dto - package net.sourceforge.seqware.webservice.dto
 
net.sourceforge.seqware.webservice.resources - package net.sourceforge.seqware.webservice.resources
 
net.sourceforge.seqware.webservice.resources.filters - package net.sourceforge.seqware.webservice.resources.filters
 
net.sourceforge.seqware.webservice.resources.queries - package net.sourceforge.seqware.webservice.resources.queries
 
net.sourceforge.seqware.webservice.resources.tables - package net.sourceforge.seqware.webservice.resources.tables
 
net.sourceforge.solexatools - package net.sourceforge.solexatools
 
net.sourceforge.solexatools.authentication - package net.sourceforge.solexatools.authentication
 
net.sourceforge.solexatools.util - package net.sourceforge.solexatools.util
 
net.sourceforge.solexatools.validation - package net.sourceforge.solexatools.validation
 
net.sourceforge.solexatools.webapp.controller - package net.sourceforge.solexatools.webapp.controller
 
net.sourceforge.solexatools.webapp.metamodel - package net.sourceforge.solexatools.webapp.metamodel
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
newBuilder(QESupporting.AtomPB) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
newBuilder(QESupporting.FeatureAtomPB) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
newBuilder(QESupporting.FSGIDPB) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
newBuilder(QESupporting.SGIDPB) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
newBuilder(QESupporting.TagPB) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
newBuilder(QueryEngine.ACLPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
newBuilder(QueryEngine.FeatureListPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
newBuilder(QueryEngine.FeaturePB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
newBuilder(QueryEngine.FeatureSetPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
newBuilder(QueryEngine.GroupPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
newBuilder(QueryEngine.MoleculePB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
newBuilder(QueryEngine.PluginPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
newBuilder(QueryEngine.PluginRunPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
newBuilder(QueryEngine.ReferencePB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
newBuilder(QueryEngine.ReferenceSetPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
newBuilder(QueryEngine.TagSetPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
newBuilder(QueryEngine.UserPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
newBuilder() - Static method in class com.github.seqware.queryengine.model.Feature
newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.FeatureList
newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.hbasemrlazy.MRLazyFeatureSet
newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryPlugin
newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference
Create a new Reference builder
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet
newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.interfaces.ACL
Create a new ACL builder, this is needed to add ne
newBuilder() - Static method in class com.github.seqware.queryengine.model.PluginRun
newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.Tag
Create a new ACL builder
newBuilder() - Static method in class com.github.seqware.queryengine.model.User
Create a new ACL builder
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
NewSeqwareStyle - Annotation Type in net.sourceforge.seqware.pipeline.module.ann
This Annotation is used to tag a ModuleInterface.
newStudyType - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE
 
newSynonym(Synonym) - Method in class com.github.seqware.queryengine.util.obo.OboFileHandlerHack
next() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.FeatureScanIterator
 
next() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterator
 
next() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl.TagValueIterator
 
next() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.BatchedRowFeatureListsIterator
 
next() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.ConsolidatedFeatureIterator
 
next() - Method in class com.github.seqware.queryengine.util.SeqWareIterator
Super method for dealing with database iterator specifics, such as closing the DB-iterator when no more data is available.
next() - Method in class com.github.seqware.queryengine.util.SGIDIterable.SGIDIterator
 
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator
next.
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator
next.
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator
next.
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator
next.
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator
next.
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator
next.
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator
next.
nextId() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
nextId.
nextImpl() - Method in class com.github.seqware.queryengine.util.InMemoryIterator
Implementation of next().
nextImpl() - Method in class com.github.seqware.queryengine.util.SeqWareIterator
Implementation of next().
nextInvitationCode() - Method in class net.sourceforge.seqware.common.invitation.RandomInvitationCode
nextInvitationCode.
nextInvitationCode() - Method in class net.sourceforge.solexatools.util.RandomInvitationCode
nextInvitationCode.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator
nextSecondaryKey.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator
Not applicable for HBase backend.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator
Not applicable for HBase backend.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.LocatableSecondaryCursorIterator
nextSecondaryKey.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator
Not applicable for Postgres backend.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator
Not applicable for Postgres backend.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator
Not applicable for Postgres backend.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator
Used to get the keys in this secondary table as strings (won't work for non string keys!).
nextSecondaryKey() - Method in interface net.sourceforge.seqware.queryengine.backend.util.SeqWareIterator
nextSecondaryKey.
NO_STRAND - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Constant NO_STRAND=0
NodeHtmlUtil - Class in net.sourceforge.solexatools.util
NodeHtmlUtil class.
NodeHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.NodeHtmlUtil
 
NoExitSecurityManager - Class in net.sourceforge.seqware.common.util
Created by IntelliJ IDEA.
NoExitSecurityManager() - Constructor for class net.sourceforge.seqware.common.util.NoExitSecurityManager
 
nominallength - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
 
nominalsdev - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
 
NonPersistentStorage - Class in com.github.seqware.queryengine.impl
Doesn't really store things anywhere, just keeps it in memory.
NonPersistentStorage(SerializationInterface) - Constructor for class com.github.seqware.queryengine.impl.NonPersistentStorage
Constructor for NonPersistentStorage.
NonPersistentStorage.ByteTypePair - Class in com.github.seqware.queryengine.impl
 
NonPersistentStorage.ByteTypePair(byte[], Class) - Constructor for class com.github.seqware.queryengine.impl.NonPersistentStorage.ByteTypePair
 
normalizeOptions(String) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner2
normalizeOptions.
NOT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant NOT=21
NOT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant NOT=21
NOT_STRANDED_VALUE - Static variable in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
NOTEQUALS - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant NOTEQUALS=22
NOTEQUALS - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant NOTEQUALS=22
notes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
 
notes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
 
notes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
 
notes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE
 
notes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS
 
notes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
 
NotFoundException - Exception in net.sourceforge.seqware.common.err
NotFoundException class.
NotFoundException() - Constructor for exception net.sourceforge.seqware.common.err.NotFoundException
Constructor for NotFoundException.
NotFoundException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.NotFoundException
Constructor for NotFoundException.
NotFoundException(String) - Constructor for exception net.sourceforge.seqware.common.err.NotFoundException
Constructor for NotFoundException.
NotFoundException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.NotFoundException
Constructor for NotFoundException.
NOTIMPLEMENTED - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant NOTIMPLEMENTED=-1
NS - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
NULL - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant NULL=-99
NullBeanUtils - Class in net.sourceforge.seqware.common.util
NullBeanUtils class.
NullBeanUtils() - Constructor for class net.sourceforge.seqware.common.util.NullBeanUtils
 
NULLIZYGOUS - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant NULLIZYGOUS=4
NUMBER_THREADS_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
Constant NUMBER_THREADS_PARAM='t'
numberChannels - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
 
numberoflevels - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
 
numberofreadsperspot - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
 

O

objectCreated(Atom) - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Called by Atoms when they are successfully created thus becoming dirty, and needing to be written to the database.
objectCreated(Atom) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Called by Atoms when they are successfully created thus becoming dirty, and needing to be written to the database.
ObjectFactory - Class in net.sourceforge.seqware.queryengine.webservice.model
This object contains factory methods for each Java content interface and Java element interface generated in the net.sourceforge.seqware.queryengine.webservice.model package.
ObjectFactory() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: net.sourceforge.seqware.queryengine.webservice.model
objectToEntry(Object, TupleOutput) - Method in class com.github.seqware.queryengine.impl.tuplebinderIO.FeatureTB
objectToEntry(Object, TupleOutput) - Method in class com.github.seqware.queryengine.impl.tuplebinderIO.SGIDTB
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.ConsequenceTB
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.ContigPositionTB
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.CoverageTB
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.FeatureTB
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.StringIdTB
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.TagTB
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.VariantTB
OboFileHandlerHack - Class in com.github.seqware.queryengine.util.obo
The BioJava 1.8.1 package does not seem to handle Synonyms correctly, need to keep track of them separately
OboFileHandlerHack(Ontology) - Constructor for class com.github.seqware.queryengine.util.obo.OboFileHandlerHack
Constructor for OboFileHandlerHack.
OBOImporter - Class in com.github.seqware.queryengine.system.importers
Quick and dirty OBO file importer.
OBOImporter() - Constructor for class com.github.seqware.queryengine.system.importers.OBOImporter
Constructor for OBOImporter.
OboParser - Class in com.github.seqware.queryengine.util.obo
Copied from BioJava 1.8.1 Legacy org.biojava.ontology.io.OboParser
OboParser() - Constructor for class com.github.seqware.queryengine.util.obo.OboParser
 
OICRLdapAuthentication - Class in net.sourceforge.solexatools.authentication
This authentication plugin allows the SeqWare Portal to authenticate against the Ontario Institute for Cancer Research (OICR) LDAP server.
OICRLdapAuthentication() - Constructor for class net.sourceforge.solexatools.authentication.OICRLdapAuthentication
 
OID - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
Constant OID=0
OID - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
Constant OID=0
OID - Static variable in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Constant OID=0
okTo - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
OldSeqwareException - Exception in net.sourceforge.seqware.common.err
This exception wraps the old seqware exception code User: Xiaoshu Wang (xiao@renci.org) Date: 9/6/11 Time: 2:38 PM
OldSeqwareException() - Constructor for exception net.sourceforge.seqware.common.err.OldSeqwareException
Constructor for OldSeqwareException.
OldSeqwareException(String) - Constructor for exception net.sourceforge.seqware.common.err.OldSeqwareException
Constructor for OldSeqwareException.
OldSeqwareException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.OldSeqwareException
Constructor for OldSeqwareException.
OldSeqwareException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.OldSeqwareException
Constructor for OldSeqwareException.
onSubmit(HttpServletRequest, HttpServletResponse, Object, BindException) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
Handles the user's request to submit a new study.
onSubmit(HttpServletRequest, HttpServletResponse, Object, BindException) - Method in class net.sourceforge.solexatools.webapp.controller.LoginController
oozie_working_dir - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
OozieJavaJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object
 
OozieJavaJob(AbstractJob, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJavaJob
 
OozieJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object
 
OozieJob(AbstractJob, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
OoziePerlJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object
 
OoziePerlJob(AbstractJob, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OoziePerlJob
 
OozieProvisionFileJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object
 
OozieProvisionFileJob(AbstractJob, SqwFile, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob
 
OozieWorkflowEngine - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.oozie
 
OozieWorkflowEngine(AbstractWorkflowDataModel) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowEngine
 
OozieWorkflowXmlGenerator - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.oozie
 
OozieWorkflowXmlGenerator() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.OozieWorkflowXmlGenerator
 
OozieXML2Dot - Class in net.sourceforge.seqware.pipeline.plugins
 
OozieXML2Dot() - Constructor for class net.sourceforge.seqware.pipeline.plugins.OozieXML2Dot
 
OpenInvoiceController - Class in net.sourceforge.solexatools.webapp.controller
OpenInvoiceController class.
OpenInvoiceController() - Constructor for class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController
Constructor for OpenInvoiceController.
OptionParsing - Class in net.sourceforge.seqware.common.util.configtools
Created by IntelliJ IDEA.
OptionParsing() - Constructor for class net.sourceforge.seqware.common.util.configtools.OptionParsing
 
options - Variable in class net.sourceforge.seqware.pipeline.decider.Decider
 
options - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
options - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
options - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
options - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
options - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory
 
options - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
OR - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant OR=23
OR - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant OR=23
org.apache.commons.cli - package org.apache.commons.cli
 
Organism - Class in net.sourceforge.seqware.common.model
Organism class.
Organism() - Constructor for class net.sourceforge.seqware.common.model.Organism
Constructor for Organism.
ORGANISM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
OrganismDAO - Interface in net.sourceforge.seqware.common.dao
OrganismDAO interface.
OrganismDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
OrganismDAOHibernate class.
OrganismDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate
Constructor for OrganismDAOHibernate.
OrganismDto - Class in net.sourceforge.seqware.webservice.dto
 
OrganismDto() - Constructor for class net.sourceforge.seqware.webservice.dto.OrganismDto
 
OrganismList - Class in net.sourceforge.seqware.common.model.lists
OrganismList class.
OrganismList() - Constructor for class net.sourceforge.seqware.common.model.lists.OrganismList
Constructor for OrganismList.
OrganismResource - Class in net.sourceforge.seqware.webservice.resources.tables
ExperimentResource class.
OrganismResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.OrganismResource
Constructor for ExperimentResource.
OrganismService - Interface in net.sourceforge.seqware.common.business
OrganismService interface.
OrganismServiceImpl - Class in net.sourceforge.seqware.common.business.impl
OrganismServiceImpl class.
OrganismServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl
Constructor for OrganismServiceImpl.
orientation - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
 
originalFileName - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
OUTPUT_FILE_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
Constant OUTPUT_FILE_PARAM='o'
outputDir - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
outputDir - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
outputFeatureInVCF(StringBuffer, Feature) - Static method in class com.github.seqware.queryengine.system.exporters.VCFDumper
outputFeatureInVCF.
OUTPUTFILE_PARAM - Static variable in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper
Constant OUTPUTFILE_PARAM='o'
outputLogString(boolean, WorkflowRunReportRow, StringBuilder) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource
outputLogString.
outputSize - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
outputZip - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
OwnerDto - Class in net.sourceforge.seqware.webservice.dto
 
OwnerDto() - Constructor for class net.sourceforge.seqware.webservice.dto.OwnerDto
 

P

packageBundle(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
packageBundle.
packageBundleToS3(File, String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
packageBundleToS3.
PAD - Static variable in class com.github.seqware.queryengine.impl.HBaseStorage
Constant PAD=15
PAD - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
Constant PAD=15
padZeros(int, int) - Static method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
padZeros.
PAGE_NUM - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant PAGE_NUM="page"
PAGE_NUM - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant PAGE_NUM="page"
PageInfo - Class in net.sourceforge.solexatools.util
PageInfo class.
PageInfo() - Constructor for class net.sourceforge.solexatools.util.PageInfo
Constructor for PageInfo.
PaginationUtil - Class in net.sourceforge.solexatools.util
PaginationUtil class.
PaginationUtil() - Constructor for class net.sourceforge.solexatools.util.PaginationUtil
 
paired - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
 
parameters - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
PARAMETERS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
params - Variable in class net.sourceforge.seqware.pipeline.decider.Decider
 
params - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
parent - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
PARENT_SAMPLE_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant PARENT_SAMPLE_ATTRIBUTES="Header.PARENT_SAMPLE_ATTRIBUTES.getTitl"{trunked}
PARENT_SAMPLE_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant PARENT_SAMPLE_NAME="Header.PARENT_SAMPLE_NAME.getTitle()"
PARENT_SAMPLE_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant PARENT_SAMPLE_SWA="Header.PARENT_SAMPLE_SWA.getTitle()"
PARENT_SAMPLE_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant PARENT_SAMPLE_TAG_PREFIX="Header.PARENT_SAMPLE_TAG_PREFIX.getTitl"{trunked}
parentAccessionFiles - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
parentAccessionFiles - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
parentAccessions - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
parentAccessions - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
parents - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
parse(String) - Static method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerParser
 
parse(String, char) - Static method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerParser
 
parse_parameters() - Method in class net.sourceforge.seqware.pipeline.decider.Decider
Parameter validation code goes here.
parse_parameters() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Parameter validation code goes here.
parse_parameters() - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
Parameter validation code goes here.
parse_parameters() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Parameter validation code goes here.
parse_parameters() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
 
parse_parameters() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
Parameter validation code goes here.
parse_parameters() - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
Parameter validation code goes here.
parse_parameters() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner
parse_parameters.
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseFields() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
parseFromFile(File) - Method in class net.sourceforge.seqware.pipeline.bundle.BundleInfo
parseFromFile.
parseMetaInfo(File) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility
Locate and parse metadata information and return a map representation
parseMiSecData(BufferedReader) - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection
 
parseMiSecFile(String) - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection
 
parseMiSecHeader(BufferedReader) - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection
 
parseOBO(BufferedReader, String, String) - Method in class com.github.seqware.queryengine.util.obo.OboParser
Parse a OBO file and return its content as a BioJava Ontology object
parseOption(Object, List<String>) - Static method in class net.sourceforge.seqware.common.util.configtools.OptionParsing
parseOption.
parseParentAccessions(Map<String, String>) - Static method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
reads a map and tries to find the parent accessions, the result is de-duplicated.
parsePegasusStatus(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
parsePegasusStatus.
parser - Variable in class net.sourceforge.seqware.pipeline.decider.Decider
 
parser - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
 
parseSGID(String) - Static method in class com.github.seqware.queryengine.system.Utility
Parse a timestamp-less SGID from a String representation
parseXml(AbstractWorkflowDataModel, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowXmlParser
parse the FTL to XML, and XML to Java
PASSWORD_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
pasteHtmlIntoParentNode(String, String, String, boolean) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil
pasteHtmlIntoParentNode.
pb2m(QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureIO
Convert from protein buffer object to model
pb2m(QueryEngine.FeatureListPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureListIO
Convert from protein buffer object to model
pb2m(QueryEngine.FeatureSetPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureSetIO
Convert from protein buffer object to model
pb2m(QESupporting.FSGIDPB) - Static method in class com.github.seqware.queryengine.impl.protobufIO.FSGIDIO
pb2m.
pb2m(QueryEngine.GroupPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.GroupIO
Convert from protein buffer object to model
pb2m(QueryEngine.PluginPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.PluginIO
Convert from protein buffer object to model
pb2m(QueryEngine.PluginRunPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.PluginRunIO
Convert from protein buffer object to model
pb2m(S) - Method in interface com.github.seqware.queryengine.impl.protobufIO.ProtobufTransferInterface
Convert from protein buffer object to model
pb2m(QueryEngine.ReferencePB) - Method in class com.github.seqware.queryengine.impl.protobufIO.ReferenceIO
Convert from protein buffer object to model
pb2m(QueryEngine.ReferenceSetPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.ReferenceSetIO
Convert from protein buffer object to model
pb2m(QESupporting.SGIDPB) - Static method in class com.github.seqware.queryengine.impl.protobufIO.SGIDIO
pb2m.
pb2m(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagIO
Convert from protein buffer object to model
pb2m(QueryEngine.TagSetPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagSetIO
Convert from protein buffer object to model
pb2m(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagSpecIO
Convert from protein buffer object to model
pb2m(QueryEngine.UserPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.UserIO
Convert from protein buffer object to model
PegasusJavaJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object
 
PegasusJavaJob(AbstractJob, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJavaJob
 
PegasusJavaSeqwareModuleJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object
 
PegasusJavaSeqwareModuleJob(AbstractJob, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJavaSeqwareModuleJob
 
PegasusJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object
a pegasusjob object and its subclasses match to the element in a dax
PegasusJob(AbstractJob, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
PegasusPerlJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object
 
PegasusPerlJob(AbstractJob, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusPerlJob
 
PegasusWorkflowEngine - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus
 
PegasusWorkflowEngine() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.PegasusWorkflowEngine
 
PENDING - Static variable in class net.sourceforge.seqware.common.metadata.Metadata
Constant PENDING="pending"
PENDING - Static variable in class net.sourceforge.seqware.pipeline.decider.Decider
Constant PENDING="pending"
PENDING - Static variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
Constant PENDING="pending"
percentage - Variable in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
 
percentage - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
performImport(SGID, int, List<String>, String, boolean, File, List<SGID>, SGID, int, SGID, String) - Static method in class com.github.seqware.queryengine.system.importers.FeatureImporter
This method does the actual work of importing given properly parsed parameters
PerlJob - Class in net.sourceforge.seqware.pipeline.workflowV2.model
 
PerlJob(String, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.PerlJob
 
permanentBundleLocation - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
PermissionsAware - Interface in net.sourceforge.seqware.common.security
PermissionsAware interface.
permissionsOfElementRequest(String) - Method in class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
Retrieve resources and list their permissions.
persist(Atom) - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager
Start managing a Atom that has been dirtied, for example, a Atom returned from a query
persist(Atom) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager
Start managing a Atom that has been dirtied, for example, a Atom returned from a query
PERSIST_VERSION_CHAINS - Static variable in interface com.github.seqware.queryengine.impl.protobufIO.ProtobufTransferInterface
Constant PERSIST_VERSION_CHAINS=false
Pfn - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object
 
Pfn() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn
 
PHASE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
PileupCoverageImporter - Class in net.sourceforge.seqware.queryengine.tools.importers
PileupCoverageImporter class.
PileupCoverageImporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.PileupCoverageImporter
 
PileupVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
PileupVariantImportWorker class.
PileupVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.PileupVariantImportWorker
Constructor for PileupVariantImportWorker.
Platform - Class in net.sourceforge.seqware.common.model
Platform class.
Platform() - Constructor for class net.sourceforge.seqware.common.model.Platform
Constructor for Platform.
platform - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
PlatformDAO - Interface in net.sourceforge.seqware.common.dao
PlatformDAO interface.
PlatformDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
PlatformDAOHibernate class.
PlatformDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate
Constructor for PlatformDAOHibernate.
PlatformList - Class in net.sourceforge.seqware.common.model.lists
PlatformList class.
PlatformList() - Constructor for class net.sourceforge.seqware.common.model.lists.PlatformList
Constructor for PlatformList.
PlatformResource - Class in net.sourceforge.seqware.webservice.resources.tables
ExperimentResource class.
PlatformResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.PlatformResource
Constructor for ExperimentResource.
PlatformService - Interface in net.sourceforge.seqware.common.business
PlatformService interface.
PlatformServiceImpl - Class in net.sourceforge.seqware.common.business.impl
PlatformServiceImpl class.
PlatformServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl
Constructor for PlatformServiceImpl.
Plugin - Interface in com.github.seqware.queryengine.model
An Plugin object groups pluginrun events that are created by software suites or related tools.
Plugin - Class in net.sourceforge.seqware.pipeline.plugin
Abstract Plugin class.
Plugin() - Constructor for class net.sourceforge.seqware.pipeline.plugin.Plugin
Constructor for Plugin.
Plugin.Builder - Class in com.github.seqware.queryengine.model
 
Plugin.Builder() - Constructor for class com.github.seqware.queryengine.model.Plugin.Builder
 
PluginInterface - Interface in com.github.seqware.queryengine.plugins
This will describe the interface custom plugins must conform to.
PluginInterface - Interface in net.sourceforge.seqware.pipeline.plugin
PluginInterface interface.
PluginInterface.ResultMechanism - Enum in com.github.seqware.queryengine.plugins
 
PluginInterface.ReturnValue - Class in com.github.seqware.queryengine.plugins
 
PluginInterface.ReturnValue() - Constructor for class com.github.seqware.queryengine.plugins.PluginInterface.ReturnValue
 
PluginIO - Class in com.github.seqware.queryengine.impl.protobufIO
PluginIO class.
PluginIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.PluginIO
 
PluginListingResource - Class in com.github.seqware.queryengine.system.rest.resources
 
PluginListingResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.PluginListingResource
 
PluginResource - Class in com.github.seqware.queryengine.system.rest.resources
Plugin resource.
PluginResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.PluginResource
 
PluginRun<ReturnType> - Class in com.github.seqware.queryengine.model
An PluginRun object represents specific calls to pluginRun components, most of which will be implemented as an pluginRun plug-in on the backend.
PluginRun() - Constructor for class com.github.seqware.queryengine.model.PluginRun
Create a new pluginrun
PluginRun.Builder - Class in com.github.seqware.queryengine.model
 
PluginRun.Builder() - Constructor for class com.github.seqware.queryengine.model.PluginRun.Builder
 
PLUGINRUNIDS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
PluginRunIO - Class in com.github.seqware.queryengine.impl.protobufIO
Place-holder
PluginRunIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.PluginRunIO
 
PluginRunListingResource - Class in com.github.seqware.queryengine.system.rest.resources
 
PluginRunListingResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.PluginRunListingResource
 
PluginRunner - Class in net.sourceforge.seqware.pipeline.runner
PluginRunner class.
PluginRunner() - Constructor for class net.sourceforge.seqware.pipeline.runner.PluginRunner
 
PluginRunnerInterface<ResultType> - Interface in com.github.seqware.queryengine.plugins
Base interface for plug-in runners.
PluginRunResource - Class in com.github.seqware.queryengine.system.rest.resources
PluginRun resource.
PluginRunResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.PluginRunResource
 
PLUS_STRAND - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Constant PLUS_STRAND=1
pmi - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
position - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
position - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
position - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
position - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
position - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
PositionSeparator - Static variable in class com.github.seqware.queryengine.util.FSGID
Constant PositionSeparator=":"
POSITIVE_VALUE - Static variable in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
post(Representation) - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter
post(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessResource
Poster - Class in com.github.seqware.queryengine.tutorial
This is a quick and dirty sample application built on top of our API, created for Poster testing.
Poster(String[]) - Constructor for class com.github.seqware.queryengine.tutorial.Poster
Constructor for Poster.
PosterSGE - Class in com.github.seqware.queryengine.tutorial
This is a quick and dirty application built on top of our API, created for Poster testing.
PosterSGE(String[]) - Constructor for class com.github.seqware.queryengine.tutorial.PosterSGE
Constructor for PosterSGE.
PosterStatCompiler - Class in com.github.seqware.queryengine.tutorial
This program compiles information generated by the Poster class.
PosterStatCompiler() - Constructor for class com.github.seqware.queryengine.tutorial.PosterStatCompiler
 
PostgresModelIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators
An interator on top of the standard Java SQL iterator
PostgresModelIterator(ResultSet, TupleBinding, int, LargeObjectManager) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator
Constructor for PostgresModelIterator.
PostgreSQLBulkWriterStore - Class in net.sourceforge.seqware.queryengine.backend.store.impl
PostgreSQLBulkWriterStore class.
PostgreSQLBulkWriterStore() - Constructor for class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
 
PostgreSQLStore - Class in net.sourceforge.seqware.queryengine.backend.store.impl
PostgreSQLStore class.
PostgreSQLStore() - Constructor for class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
 
PostgresTagModelIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators
An interator on top of the standard Java SQL iterator
PostgresTagModelIterator(ResultSet, PostgreSQLStore) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator
Constructor for PostgresTagModelIterator.
PostgresVariantModelIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators
An interator on top of the standard Java SQL iterator
PostgresVariantModelIterator(ResultSet, PostgreSQLStore) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator
Constructor for PostgresVariantModelIterator.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentResource
postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileResource
postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.IusResource
postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneResource
postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessResource
postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleResource
postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunResource
postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource
postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamResource
postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueResource
postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowResource
postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource
postJaxb.
postRun(Representation) - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter
postRun.
PRAGMA_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
PRECEDINGID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
PRECEDINGID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
PREDICATE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
prefix - Static variable in class com.github.seqware.queryengine.model.FeatureSet
Constant prefix="FeatureSet"
prefix - Static variable in interface com.github.seqware.queryengine.model.Group
Constant prefix="Group"
prefix - Static variable in class com.github.seqware.queryengine.model.impl.FeatureList
Constant prefix="Feature"
prefix - Static variable in interface com.github.seqware.queryengine.model.Plugin
Constant prefix="Plugin"
prefix - Static variable in class com.github.seqware.queryengine.model.PluginRun
Constant prefix="PluginRun"
prefix - Static variable in interface com.github.seqware.queryengine.model.Reference
Constant prefix="Reference"
prefix - Static variable in interface com.github.seqware.queryengine.model.ReferenceSet
Constant prefix="ReferenceSet"
prefix - Static variable in class com.github.seqware.queryengine.model.Tag
Constant prefix="Tag"
prefix - Static variable in interface com.github.seqware.queryengine.model.TagSet
Constant prefix="TagSet"
prefix - Static variable in class com.github.seqware.queryengine.model.User
Constant prefix="User"
prepareData(WorkflowInfo, String, ArrayList<String>, Map<String, String>, boolean, ArrayList<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
prepareData.
prependToFilePath(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
prettyPrint(String) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools
prettyPrint.
print(Writer, ReturnValue, String, boolean, FileMetadata) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
print(Writer, ReturnValue, String, boolean, FileMetadata, boolean) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Prints a line to the Excel spreadsheet.
print(String) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
print.
print(String) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
print.
printAndAppendtoStderr(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
printAndAppendtoStderr.
printAndAppendtoStderr(String) - Method in class net.sourceforge.seqware.pipeline.runner.Runner
printAndAppendtoStderr.
printAndAppendtoStdout(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
printAndAppendtoStdout.
printAndAppendtoStdout(String) - Method in class net.sourceforge.seqware.pipeline.runner.Runner
printAndAppendtoStdout.
printAndAppendtoString(String, String) - Static method in class net.sourceforge.seqware.common.util.processtools.stderr.StdErr
printAndAppendtoString.
printf(String, Object...) - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter
 
printFileMetadata(ReturnValue, FileMetadata) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
printHeader(Writer, boolean) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
printHeader(Writer, boolean, boolean) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Print the header of the Excel spreadsheet to file.
println(String) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
println.
printTSVFile(Writer, boolean, List<ReturnValue>, String) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
printTSVFile(Writer, boolean, List<ReturnValue>, String, boolean) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
printTSVFile.
process(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
process.
process(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageStatsProcessor
process.
process(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.MismatchConsequenceReportProcessor
process.
process(Object) - Method in interface net.sourceforge.seqware.queryengine.tools.iterators.processors.ProcessorInterface
process.
process(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
process.
process(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantStatsProcessor
process.
processArgs(Option, ListIterator) - Method in class org.apache.commons.cli.HackedPosixParser
processExitStatus - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
ProcessIdProcessResource - Class in net.sourceforge.seqware.webservice.resources.queries
ProcessIdProcessResource class.
ProcessIdProcessResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.ProcessIdProcessResource
Constructor for ProcessIdProcessResource.
ProcessIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
ProcessIDResource class.
ProcessIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ProcessIDResource
Constructor for ProcessIDResource.
Processing - Class in net.sourceforge.seqware.common.model
 
Processing() - Constructor for class net.sourceforge.seqware.common.model.Processing
Constructor for Processing.
PROCESSING - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant PROCESSING=100
processing - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
PROCESSING_ALGO - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant PROCESSING_ALGO="Header.PROCESSING_ALGO.getTitle()"
PROCESSING_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant PROCESSING_ATTRIBUTES="Header.PROCESSING_ATTRIBUTES.getTitle()"
PROCESSING_DATE - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant PROCESSING_DATE="Header.PROCESSING_DATE.getTitle()"
processing_event_to_task_group(int, int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
processing_event_to_task_group.
processing_event_to_task_group(int, int[], int[], String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
processing_event_to_task_group.
processing_event_to_task_group(int, int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
processing_event_to_task_group.
processing_event_to_task_group(int, int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
processing_event_to_task_group.
PROCESSING_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
Constant PROCESSING_PREFIX="ae_"
PROCESSING_SWID - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant PROCESSING_SWID="Header.PROCESSING_SWID.getTitle()"
PROCESSING_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant PROCESSING_TAG_PREFIX="Header.PROCESSING_TAG_PREFIX.getTitle()"
processingAccession - Variable in class net.sourceforge.seqware.pipeline.module.Module
 
ProcessingAttribute - Class in net.sourceforge.seqware.common.model
ProcessingAttribute generated by hbm2java
ProcessingAttribute() - Constructor for class net.sourceforge.seqware.common.model.ProcessingAttribute
Constructor for ProcessingAttribute.
ProcessingAttribute(int, Processing) - Constructor for class net.sourceforge.seqware.common.model.ProcessingAttribute
Constructor for ProcessingAttribute.
ProcessingAttribute(int, Processing, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.ProcessingAttribute
Constructor for ProcessingAttribute.
ProcessingAttributeDAO - Interface in net.sourceforge.seqware.common.dao
ProcessingAttributeDAO interface.
ProcessingAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ProcessingAttributeDAOHibernate class.
ProcessingAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate
 
ProcessingController - Class in net.sourceforge.solexatools.webapp.controller
SequencerRunController
ProcessingController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ProcessingController
Constructor for ProcessingController.
ProcessingController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.ProcessingController
Constructor for ProcessingController.
ProcessingDAO - Interface in net.sourceforge.seqware.common.dao
ProcessingDAO interface.
ProcessingDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ProcessingDAOHibernate class.
ProcessingDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
Constructor for ProcessingDAOHibernate.
ProcessingDataStructure2Dot - Class in net.sourceforge.seqware.pipeline.plugins
 
ProcessingDataStructure2Dot() - Constructor for class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot
 
ProcessingExperiments - Class in net.sourceforge.seqware.common.model
ProcessingExperiments generated by hbm2java
ProcessingExperiments() - Constructor for class net.sourceforge.seqware.common.model.ProcessingExperiments
Constructor for ProcessingExperiments.
ProcessingExperiments(int, Processing, Experiment) - Constructor for class net.sourceforge.seqware.common.model.ProcessingExperiments
Constructor for ProcessingExperiments.
ProcessingExperiments(int, Processing, Experiment, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingExperiments
Constructor for ProcessingExperiments.
ProcessingExperimentsDAO - Interface in net.sourceforge.seqware.common.dao
ProcessingExperimentsDAO interface.
ProcessingExperimentsDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ProcessingExperimentsDAOHibernate class.
ProcessingExperimentsDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate
 
ProcessingExperimentsService - Interface in net.sourceforge.seqware.common.business
ProcessingExperimentsService interface.
ProcessingExperimentsServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ProcessingExperimentsServiceImpl class.
ProcessingExperimentsServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
 
ProcessingIus - Class in net.sourceforge.seqware.common.model
ProcessingIus generated by hbm2java
ProcessingIus() - Constructor for class net.sourceforge.seqware.common.model.ProcessingIus
Constructor for ProcessingIus.
ProcessingIus(int, IUS, Processing) - Constructor for class net.sourceforge.seqware.common.model.ProcessingIus
Constructor for ProcessingIus.
ProcessingIus(int, IUS, Processing, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingIus
Constructor for ProcessingIus.
ProcessingIUSDAO - Interface in net.sourceforge.seqware.common.dao
ProcessingIUSDAO interface.
ProcessingIUSDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ProcessingIUSDAOHibernate class.
ProcessingIUSDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate
 
ProcessingIUSService - Interface in net.sourceforge.seqware.common.business
ProcessingIUSService interface.
ProcessingIUSServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ProcessingIUSServiceImpl class.
ProcessingIUSServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
 
ProcessingLanes - Class in net.sourceforge.seqware.common.model
ProcessingLanes generated by hbm2java
ProcessingLanes() - Constructor for class net.sourceforge.seqware.common.model.ProcessingLanes
Constructor for ProcessingLanes.
ProcessingLanes(int, Processing, Lane) - Constructor for class net.sourceforge.seqware.common.model.ProcessingLanes
Constructor for ProcessingLanes.
ProcessingLanes(int, Processing, Lane, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingLanes
Constructor for ProcessingLanes.
ProcessingLanesDAO - Interface in net.sourceforge.seqware.common.dao
ProcessingLanesDAO interface.
ProcessingLanesDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ProcessingLanesDAOHibernate class.
ProcessingLanesDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate
 
ProcessingLanesService - Interface in net.sourceforge.seqware.common.business
ProcessingLanesService interface.
ProcessingLanesServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ProcessingLanesServiceImpl class.
ProcessingLanesServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
 
ProcessingList - Class in net.sourceforge.seqware.common.model.lists
ProcessingList class.
ProcessingList() - Constructor for class net.sourceforge.seqware.common.model.lists.ProcessingList
Constructor for ProcessingList.
ProcessingRelationship - Class in net.sourceforge.seqware.common.model
ProcessingRelationship generated by hbm2java
ProcessingRelationship() - Constructor for class net.sourceforge.seqware.common.model.ProcessingRelationship
Constructor for ProcessingRelationship.
ProcessingRelationship(int) - Constructor for class net.sourceforge.seqware.common.model.ProcessingRelationship
Constructor for ProcessingRelationship.
ProcessingRelationship(int, Processing, Processing, String) - Constructor for class net.sourceforge.seqware.common.model.ProcessingRelationship
Constructor for ProcessingRelationship.
ProcessingRelationshipDAO - Interface in net.sourceforge.seqware.common.dao
ProcessingRelationshipDAO interface.
ProcessingRelationshipDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ProcessingRelationshipDAOHibernate class.
ProcessingRelationshipDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate
 
ProcessingRelationshipService - Interface in net.sourceforge.seqware.common.business
ProcessingRelationshipService interface.
ProcessingRelationshipServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ProcessingRelationshipServiceImpl class.
ProcessingRelationshipServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
 
ProcessingResource - Class in net.sourceforge.seqware.queryengine.webservice.view
ProcessingResource class.
ProcessingResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.ProcessingResource
 
ProcessingSamples - Class in net.sourceforge.seqware.common.model
ProcessingSamples generated by hbm2java
ProcessingSamples() - Constructor for class net.sourceforge.seqware.common.model.ProcessingSamples
Constructor for ProcessingSamples.
ProcessingSamples(int, Processing, Sample) - Constructor for class net.sourceforge.seqware.common.model.ProcessingSamples
Constructor for ProcessingSamples.
ProcessingSamples(int, Processing, Sample, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingSamples
Constructor for ProcessingSamples.
ProcessingSamplesDAO - Interface in net.sourceforge.seqware.common.dao
ProcessingSamplesDAO interface.
ProcessingSamplesDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ProcessingSamplesDAOHibernate class.
ProcessingSamplesDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate
 
ProcessingSamplesService - Interface in net.sourceforge.seqware.common.business
ProcessingSamplesService interface.
ProcessingSamplesServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ProcessingSamplesServiceImpl class.
ProcessingSamplesServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
 
processingsCount(Sample) - Static method in class net.sourceforge.solexatools.util.TagUtils
Returns count of the Sample related Workflow Runs.
ProcessingSequencerRuns - Class in net.sourceforge.seqware.common.model
ProcessingSequencerRuns generated by hbm2java
ProcessingSequencerRuns() - Constructor for class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
Constructor for ProcessingSequencerRuns.
ProcessingSequencerRuns(int, Processing, SequencerRun) - Constructor for class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
Constructor for ProcessingSequencerRuns.
ProcessingSequencerRuns(int, Processing, SequencerRun, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
Constructor for ProcessingSequencerRuns.
ProcessingSequencerRunsDAO - Interface in net.sourceforge.seqware.common.dao
ProcessingSequencerRunsDAO interface.
ProcessingSequencerRunsDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ProcessingSequencerRunsDAOHibernate class.
ProcessingSequencerRunsDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate
 
ProcessingSequencerRunsService - Interface in net.sourceforge.seqware.common.business
ProcessingSequencerRunsService interface.
ProcessingSequencerRunsServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ProcessingSequencerRunsServiceImpl class.
ProcessingSequencerRunsServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
 
ProcessingService - Interface in net.sourceforge.seqware.common.business
ProcessingService interface.
ProcessingServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ProcessingServiceImpl class.
ProcessingServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
Constructor for ProcessingServiceImpl.
ProcessingSetupController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
ProcessingSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
Constructor for ProcessingSetupController.
ProcessingStructureResource - Class in net.sourceforge.seqware.webservice.resources.tables
 
ProcessingStructureResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ProcessingStructureResource
 
ProcessingStudies - Class in net.sourceforge.seqware.common.model
ProcessingStudies generated by hbm2java
ProcessingStudies() - Constructor for class net.sourceforge.seqware.common.model.ProcessingStudies
Constructor for ProcessingStudies.
ProcessingStudies(int, Processing, Study) - Constructor for class net.sourceforge.seqware.common.model.ProcessingStudies
Constructor for ProcessingStudies.
ProcessingStudies(int, Processing, Study, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingStudies
Constructor for ProcessingStudies.
ProcessingStudiesDAO - Interface in net.sourceforge.seqware.common.dao
ProcessingStudiesDAO interface.
ProcessingStudiesDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ProcessingStudiesDAOHibernate class.
ProcessingStudiesDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate
 
ProcessingStudiesService - Interface in net.sourceforge.seqware.common.business
ProcessingStudiesService interface.
ProcessingStudiesServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ProcessingStudiesServiceImpl class.
ProcessingStudiesServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
 
ProcessingTaskGroup - Class in net.sourceforge.seqware.common.metadata.ProcessingTaskGroup
Standalone application to insert a new processing task group into the database.
ProcessingTaskGroup() - Constructor for class net.sourceforge.seqware.common.metadata.ProcessingTaskGroup.ProcessingTaskGroup
 
ProcessorInterface - Interface in net.sourceforge.seqware.queryengine.tools.iterators.processors
ProcessorInterface interface.
ProcessResource - Class in net.sourceforge.seqware.webservice.resources.tables
ProcessResource class.
ProcessResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ProcessResource
Constructor for ProcessResource.
processTemplate(String[], String, String, Map<String, String>, String[]) - Method in class net.sourceforge.seqware.pipeline.daxgenerator.Daxgenerator
processTemplate.
ProcessTools - Class in net.sourceforge.seqware.common.util.processtools
Sleep for N seconds.
ProcessTools() - Constructor for class net.sourceforge.seqware.common.util.processtools.ProcessTools
 
processVCFTagSpec(String, TagSet, CreateUpdateManager) - Static method in class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker
processVCFTagSpec.
PROGRAMFAILED - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant PROGRAMFAILED=1
Project - Class in net.sourceforge.seqware.common.model
Project class.
Project() - Constructor for class net.sourceforge.seqware.common.model.Project
Constructor for Project.
ProjectDAO - Interface in net.sourceforge.seqware.common.dao
ProjectDAO interface.
ProjectDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ProjectDAOHibernate class.
ProjectDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate
Constructor for ProjectDAOHibernate.
projectid - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
 
ProjectService - Interface in net.sourceforge.seqware.common.business
ProjectService interface.
ProjectServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ProjectServiceImpl class.
ProjectServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
Constructor for ProjectServiceImpl.
promptBoolean(String, Boolean) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
promptForExperiment(String[]) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
promptForFields(String[]) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
promptForIUS(String[]) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
promptForLane(String[]) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
promptForSample(String[]) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
promptForSequencerRun(String[]) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
promptForStudy(String[]) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
promptInteger(String, Integer) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
promptString(String, String) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata
 
PropagateOwnership - Class in net.sourceforge.seqware.common.hibernate
Should only be used for one query and then discarded and re-instantiated.
PropagateOwnership() - Constructor for class net.sourceforge.seqware.common.hibernate.PropagateOwnership
Constructor for PropagateOwnership.
protect - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
 
ProtobufSerialization - Class in com.github.seqware.queryengine.impl
ProtobufSerialization class.
ProtobufSerialization() - Constructor for class com.github.seqware.queryengine.impl.ProtobufSerialization
 
ProtobufTransferInterface<S extends com.google.protobuf.Message,T extends Atom> - Interface in com.github.seqware.queryengine.impl.protobufIO
Interface for conversion from protein buffer auto-generated objects to model and vice versa
ProvisionDependenciesBundle - Class in net.sourceforge.seqware.pipeline.modules.utilities
Purpose: This module takes a software bundle and unzips it to the temporary directory.
ProvisionDependenciesBundle() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
 
provisionFile(String, String) - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
This method was tested with: # local to local ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles -- --input-file /tmp/foo --output-dir /tmp/tmp2 # local to S3 ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles -- --input-file /tmp/foo --output-dir s3://seqware.bundles/dependencies/data # http to local ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles -- --input-file https://s3.amazonaws.com/seqware.bundles/dependencies/data/AboutStacks.pdf.zip --output-dir /tmp/tmp2 # http to S3 ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles -- --input-file https://s3.amazonaws.com/seqware.bundles/dependencies/data/AboutStacks.pdf.zip --output-dir s3://seqware.bundles/dependencies/noarch # S3 to local ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles -- --input-file s3://seqware.bundles/dependencies/data/AboutStacks.pdf.zip --output-dir /tmp/tmp2 # S3 to S3 ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles -- --input-file s3://seqware.bundles/dependencies/data/AboutStacks.pdf.zip --output-dir s3://seqware.bundles/dependencies/noarch
provisionFile(String, String, boolean, ArrayList<FileMetadata>, boolean) - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
provisionFile.
ProvisionFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities
Purpose: This module takes one or more inputs (S3 URL, HTTP/HTTPS URL, or local file path) and copies the file to the specified output (S3 bucket URL, HTTP/HTTPS URL, or local directory path).
ProvisionFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
ProvisionFilesJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object
 
ProvisionFilesJob(AbstractJob, String, SqwFile, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob
 
ProvisionFilesUtil - Class in net.sourceforge.seqware.common.util.filetools
ProvisionFilesUtil class.
ProvisionFilesUtil() - Constructor for class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Default ctor.
ProvisionFilesUtil(boolean) - Constructor for class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Set verbose mode ctor.
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.IusIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource
put(HttpServletRequest) - Static method in class net.sourceforge.solexatools.Debug
put.
put(String) - Static method in class net.sourceforge.solexatools.Debug
put.
put(Object, String) - Static method in class net.sourceforge.solexatools.Debug
put.
putConsequence(Consequence) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
putConsequence.
putConsequence(Consequence, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
putConsequence.
putConsequence(Consequence, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
putConsequence.
putConsequence(Consequence) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
putConsequence.
putConsequence(Consequence) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
putConsequence.
putConsequence(Consequence, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
putConsequence.
putConsequence(Consequence) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
putConsequence.
putConsequence(Consequence, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
putConsequence.
putConsequence(Consequence, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
putConsequence.
putConsequence(Consequence) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
putConsequence.
putConsequence(Consequence, boolean) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
putConsequence.
putConsequence(Consequence) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
putConsequence.
putCoverage(Integer, Integer) - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage
putCoverage.
putCoverage(Coverage) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
putCoverage.
putCoverage(Coverage, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
putCoverage.
putCoverage(Coverage) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
putCoverage.
putCoverage(Coverage, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
putCoverage.
putCoverage(Coverage) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
putCoverage.
putCoverage(Coverage, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
putCoverage.
putCoverage(Coverage) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
putCoverage.
putCoverage(Coverage, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
putCoverage.
putCoverage(Coverage) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
putCoverage.
putCoverage(Coverage, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
putCoverage.
putCoverage(Coverage) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
putCoverage.
putCoverage(Coverage, boolean) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
putCoverage.
putDestination(BufferedInputStream, String, int, String, ArrayList<FileMetadata>, boolean) - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
HTTP writeback currently not supported S3 uses multi-part upload which should deal with failed uploads (maybe) I'm not really dealing with failed upload recovery here...
putFeature(FeatureSet, Feature) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
putFeature.
putFeature(Feature, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
putFeature.
putFeature(Feature) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
putFeature.
putFeature(Feature, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
putFeature.
putFeature(Feature) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
putFeature.
putFeature(Feature, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
putFeature.
putFeature(Feature) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
putFeature.
putFeature(Feature, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
putFeature.
putFeature(Feature) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
putFeature.
putFeature(Feature, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
putFeature.
putFeature(Feature) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
putFeature.
putFeature(Feature, SeqWareIterator, boolean) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
putFeature.
putFeature(Feature) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
putFeature.
putMismatch(Variant) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
putMismatch.
putMismatch(Variant, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
putMismatch.
putMismatch(Variant) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
putMismatch.
putMismatch(Variant, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
putMismatch.
putMismatch(Variant) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
putMismatch.
putMismatch(Variant, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
putMismatch.
putMismatch(Variant) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
putMismatch.
putMismatch(Variant, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
putMismatch.
putMismatch(Variant) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
putMismatch.
putMismatch(Variant, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
putMismatch.
putMismatch(Variant) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
putMismatch.
putMismatch(Variant, SeqWareIterator, boolean) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
putMismatch.
putModel(Database, TupleBinding, Model, Long, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
putModel.
putModel(String, LocatableModel, TupleBinding, HTable, HTable, HTable, String, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
FIXME: what happens if something steps on this load below and creates a timestamp that exists already? may need to look at transaction support or making this syncronized (won't matter if other client on other machine overwrites this timestamp!)
putModel(String, String, String, TupleBinding, LocatableModel) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
putModel.
putTag(Tag, Tag) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
putTag.
putToHttp() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Not supported yet.
putToS3(BufferedInputStream, String, boolean) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Copy file using reader into output.
putToS3(BufferedInputStream, String, boolean, int, int, int, int) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
putToS3(InputStream, String, boolean, Cipher, Cipher) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Copy file using reader into output.
putToS3(InputStream, String, boolean, int, int, int, int, Cipher, Cipher) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 

Q

qcreport - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
 
QE_STATUS - Static variable in class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
 
QESupporting - Class in com.github.seqware.queryengine.dto
 
QESupporting.AtomPB - Class in com.github.seqware.queryengine.dto
 
QESupporting.AtomPB.Builder - Class in com.github.seqware.queryengine.dto
 
QESupporting.AtomPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QESupporting.FeatureAtomPB - Class in com.github.seqware.queryengine.dto
 
QESupporting.FeatureAtomPB.Builder - Class in com.github.seqware.queryengine.dto
 
QESupporting.FeatureAtomPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QESupporting.FSGIDPB - Class in com.github.seqware.queryengine.dto
 
QESupporting.FSGIDPB.Builder - Class in com.github.seqware.queryengine.dto
 
QESupporting.FSGIDPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QESupporting.SGIDPB - Class in com.github.seqware.queryengine.dto
 
QESupporting.SGIDPB.Builder - Class in com.github.seqware.queryengine.dto
 
QESupporting.SGIDPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QESupporting.TagPB - Class in com.github.seqware.queryengine.dto
 
QESupporting.TagPB.Builder - Class in com.github.seqware.queryengine.dto
 
QESupporting.TagPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
qtype - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
 
qualityscorer - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
 
qualityscores - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING
 
query() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
query.
QUERY_PARAM_FILE - Static variable in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper
Constant QUERY_PARAM_FILE='p'
QUERY_PARAM_STRING - Static variable in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper
Constant QUERY_PARAM_STRING='s'
QueryDumperInterface - Interface in com.github.seqware.queryengine.system.exporters
This interface should be extended by a class that a developer wishes to use as input to the QueryVCFDumper.
QueryEngine - Class in com.github.seqware.queryengine.dto
 
QueryEngine.ACLPB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.ACLPB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.ACLPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.FeatureListPB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.FeatureListPB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.FeatureListPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.FeaturePB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.FeaturePB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.FeaturePB.StrandPB - Enum in com.github.seqware.queryengine.dto
 
QueryEngine.FeaturePBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.FeatureSetPB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.FeatureSetPB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.FeatureSetPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.GroupPB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.GroupPB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.GroupPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.MoleculePB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.MoleculePB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.MoleculePBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.PluginPB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.PluginPB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.PluginPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.PluginRunPB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.PluginRunPB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.PluginRunPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.ReferencePB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.ReferencePB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.ReferencePBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.ReferenceSetPB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.ReferenceSetPB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.ReferenceSetPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.TagSetPB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.TagSetPB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.TagSetPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngine.UserPB - Class in com.github.seqware.queryengine.dto
 
QueryEngine.UserPB.Builder - Class in com.github.seqware.queryengine.dto
 
QueryEngine.UserPBOrBuilder - Interface in com.github.seqware.queryengine.dto
 
QueryEngineService - Class in com.github.seqware.queryengine.system.rest
Mimic PingaService from https://github.com/joejimbo/genobyte/blob/master/genobyte-pinga/src/main/java/org/obiba/pinga/PingaService.java to demo web services.
QueryEngineService() - Constructor for class com.github.seqware.queryengine.system.rest.QueryEngineService
 
QueryEngineServiceConfigReader - Class in com.github.seqware.queryengine.system.rest
See http://www.tumblr.com/tagged/api?before=1327364346 .
QueryEngineServiceConfigReader(ServletConfig) - Constructor for class com.github.seqware.queryengine.system.rest.QueryEngineServiceConfigReader
 
QueryFuture<ReturnType> - Interface in com.github.seqware.queryengine.model
This interface sketches out the result that might be returned from a asynchronous query.
QueryInterface - Interface in com.github.seqware.queryengine.model
This interface allows users to access queries that are built into the query engine, as well as install/un-install plug-ins that allow the user to perform additional annotation and/or other operations (in other words, this handles the R operations from CRUD)).
QueryInterface.Location - Enum in com.github.seqware.queryengine.model
Type of location query.
queryValues - Variable in class net.sourceforge.seqware.webservice.resources.BasicResource
 
queryValues - Variable in class net.sourceforge.seqware.webservice.resources.BasicRestlet
 
QueryVCFDumper - Class in com.github.seqware.queryengine.system.exporters
Exporter using a new interface to the parameters in order to support queries triggerable from the command-line.
QueryVCFDumper() - Constructor for class com.github.seqware.queryengine.system.exporters.QueryVCFDumper
 
QUEUED - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant QUEUED=101

R

r - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
random - Variable in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
RandomInvitationCode - Class in net.sourceforge.seqware.common.invitation
RandomInvitationCode class.
RandomInvitationCode() - Constructor for class net.sourceforge.seqware.common.invitation.RandomInvitationCode
Constructor for RandomInvitationCode.
RandomInvitationCode - Class in net.sourceforge.solexatools.util
RandomInvitationCode class.
RandomInvitationCode() - Constructor for class net.sourceforge.solexatools.util.RandomInvitationCode
Constructor for RandomInvitationCode.
read(Kryo, Input) - Method in class com.github.seqware.queryengine.util.FSGID
read(Kryo, Input) - Method in class com.github.seqware.queryengine.util.SGID
READ_ATTEMPTS - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
 
READ_ATTEMPTS - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
READ_ATTEMPTS - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
READ_ATTEMPTS - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
READ_ATTEMPTS - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
readBases - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
readclass - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
 
readCount - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
reader() - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter
 
readindex - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
 
readLine() - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter
 
readLine(String, Object...) - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter
 
readPassword() - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter
 
readPassword(String, Object...) - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter
 
readspec - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
 
readsSupportingCallOne - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
readsSupportingCallThree - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
readsSupportingCallTwo - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
readTags(Model, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
readTags.
readTags(Model, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
readTags.
readtype - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
 
rebuild() - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
Rebuild the underlying set architecture.
rebuild() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
Rebuild the underlying set architecture.
rebuild() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
Rebuild the underlying set architecture.
rebuild() - Method in interface com.github.seqware.queryengine.model.interfaces.MolSetInterface
Rebuild the underlying set architecture.
recursivelyUploadDir(String, String, String, TransferManager) - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory
 
redirect() - Method in class net.sourceforge.seqware.pipeline.runner.DefaultConfig
redirect.
REDIRECT - Static variable in interface net.sourceforge.seqware.pipeline.runner.RunnerParams.Bean
 
RedirectAspect - Class in net.sourceforge.seqware.pipeline.runner
We need to clarify that there are two issues here.
RedirectAspect() - Constructor for class net.sourceforge.seqware.pipeline.runner.RedirectAspect
 
RedirectAware - Interface in net.sourceforge.seqware.pipeline.module
This module, in conjunction with the Tag and Run annotation are used to replace the old Module with the Runner code.
reduce(KEYIN, Iterable<VALUEIN>, Reducer<KEYIN, VALUEIN, KEYOUT, Writable>.Context) - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner.PluginRunnerReducer
 
reduce(REDUCEKEYIN, Iterable<REDUCEVALUEIN>, ReducerInterface<REDUCEKEYOUT, REDUCEVALUEOUT>) - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
Reduce implementation that takes mapped atoms and processes them.
reduce(FeatureSet, Iterable<FeatureSet>, ReducerInterface<FeatureSet, FeatureSet>) - Method in class com.github.seqware.queryengine.plugins.plugins.FeaturesByFilterPlugin
 
reduce(Object, Iterable<Object>, ReducerInterface<Object, Object>) - Method in class com.github.seqware.queryengine.plugins.plugins.FeatureSetCountPlugin
 
reduce(Text, Iterable<Text>, ReducerInterface<Text, Text>) - Method in class com.github.seqware.queryengine.plugins.plugins.VCFDumperPlugin
 
reduceCleanup() - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
reducerCleanup.
reduceInit() - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
reduceInit.
ReducerInterface<REDUCEKEYOUT,REDUCEVALUEOUT> - Interface in com.github.seqware.queryengine.plugins
 
Reference - Interface in com.github.seqware.queryengine.model
A reference is a particular build version such as "hg19" or "hg18".
reference - Variable in class com.github.seqware.queryengine.model.Reference.Builder
 
Reference.Builder - Class in com.github.seqware.queryengine.model
 
Reference.Builder() - Constructor for class com.github.seqware.queryengine.model.Reference.Builder
 
REFERENCE_ID_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
Constant REFERENCE_ID_PARAM='r'
referencealignment - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
 
referenceAveSeqQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
referenceBase - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
referenceCache - Variable in class com.github.seqware.queryengine.util.LazyReference
 
referenceCallQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
referenceChecked - Variable in class com.github.seqware.queryengine.util.LazyReference
 
ReferenceCreator - Class in com.github.seqware.queryengine.system
Quick and dirty ReferenceCreator.
ReferenceCreator() - Constructor for class com.github.seqware.queryengine.system.ReferenceCreator
Constructor for ReferenceCreator.
referenceId - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
REFERENCEID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
REFERENCEIDS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
ReferenceIO - Class in com.github.seqware.queryengine.impl.protobufIO
ReferenceIO class.
ReferenceIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.ReferenceIO
 
ReferenceListingResource - Class in com.github.seqware.queryengine.system.rest.resources
 
ReferenceListingResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.ReferenceListingResource
 
referenceMaxSeqQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
ReferenceResource - Class in com.github.seqware.queryengine.system.rest.resources
Reference resource.
ReferenceResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.ReferenceResource
 
ReferenceSet - Interface in com.github.seqware.queryengine.model
A ReferenceSet is a collection of references which are a collection of contigs and coordinates.
ReferenceSet.Builder - Class in com.github.seqware.queryengine.model
 
ReferenceSet.Builder() - Constructor for class com.github.seqware.queryengine.model.ReferenceSet.Builder
 
ReferenceSetIO - Class in com.github.seqware.queryengine.impl.protobufIO
ReferenceSetIO class.
ReferenceSetIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.ReferenceSetIO
 
ReferenceSetListingResource - Class in com.github.seqware.queryengine.system.rest.resources
 
ReferenceSetListingResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.ReferenceSetListingResource
 
ReferenceSetResource - Class in com.github.seqware.queryengine.system.rest.resources
ReferenceSet resource.
ReferenceSetResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.ReferenceSetResource
 
referenceSGID - Variable in class com.github.seqware.queryengine.util.LazyReference
 
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF
 
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF
 
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF
 
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF
 
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR
 
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF
 
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF
 
REFNAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
refRegex - Static variable in class com.github.seqware.queryengine.Constants
Regular Expression for suitable rowKeys
refresh(Atom) - Method in interface com.github.seqware.queryengine.backInterfaces.LowLevelBackEndInterface
Update the obj using the latest information from the back-end
refresh(Atom) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
Update the obj using the latest information from the back-end
region - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
 
registerAllExtensions(ExtensionRegistry) - Static method in class com.github.seqware.queryengine.dto.QESupporting
 
registerAllExtensions(ExtensionRegistry) - Static method in class com.github.seqware.queryengine.dto.QueryEngine
 
Registration - Class in net.sourceforge.seqware.common.model
Registration
Registration() - Constructor for class net.sourceforge.seqware.common.model.Registration
Constructor for Registration.
registration - Variable in class net.sourceforge.seqware.webservice.resources.BasicResource
 
registration - Variable in class net.sourceforge.seqware.webservice.resources.BasicRestlet
 
RegistrationController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationController class.
RegistrationController() - Constructor for class net.sourceforge.solexatools.webapp.controller.RegistrationController
Constructor for RegistrationController.
RegistrationController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.RegistrationController
Constructor for RegistrationController.
RegistrationDAO - Interface in net.sourceforge.seqware.common.dao
RegistrationDAO interface.
RegistrationDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
RegistrationDAOHibernate class.
RegistrationDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate
Constructor for RegistrationDAOHibernate.
RegistrationDTO - Class in net.sourceforge.seqware.common.model
 
RegistrationDTO() - Constructor for class net.sourceforge.seqware.common.model.RegistrationDTO
Constructor for RegistrationDTO.
RegistrationService - Interface in net.sourceforge.seqware.common.business
RegistrationService interface.
RegistrationServiceImpl - Class in net.sourceforge.seqware.common.business.impl
RegistrationServiceImpl class.
RegistrationServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
Constructor for RegistrationServiceImpl.
RegistrationSetupController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
RegistrationSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController
Constructor for RegistrationSetupController.
RegistrationValidator - Class in net.sourceforge.solexatools.validation
RegistrationValidator class.
RegistrationValidator() - Constructor for class net.sourceforge.solexatools.validation.RegistrationValidator
Constructor for RegistrationValidator.
relativeLocation - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
release - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
 
releaseLock() - Method in class com.github.seqware.queryengine.system.importers.Importer
releaseLock.
releaseLock() - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
Deprecated. releaseLock.
releaseLock() - Method in class net.sourceforge.seqware.queryengine.tools.importers.Importer
releaseLock.
releaseStore(String) - Static method in class net.sourceforge.seqware.queryengine.webservice.model.BackendPool
releaseStore.
remove() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.FeatureScanIterator
 
remove() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterator
 
remove(Feature) - Method in class com.github.seqware.queryengine.model.FeatureSet
Remove one element
remove() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl.TagValueIterator
 
remove(Feature) - Method in class com.github.seqware.queryengine.model.impl.FeatureList
remove.
remove(T) - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
Remove one element
remove(Feature) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
Remove one element
remove() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.BatchedRowFeatureListsIterator
 
remove() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.ConsolidatedFeatureIterator
 
remove(Feature) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
Remove one element
remove(T) - Method in interface com.github.seqware.queryengine.model.interfaces.MolSetInterface
Remove one element
remove() - Method in class com.github.seqware.queryengine.util.SeqWareIterator
Removal of subjects cannot be done implicitly from an iterator -- this method is not supported.
remove() - Method in class com.github.seqware.queryengine.util.SGIDIterable.SGIDIterator
 
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator
remove.
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator
Removes are unimplemented.
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator
Removes are unimplemented.
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator
Removes are unimplemented.
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator
Removes are unimplemented.
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator
Removes are unimplemented.
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator
remove.
removeFeatures(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
removeFeatures(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
removeFeatureSetIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
removeGrps(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
removePluginRunIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
removeReferenceIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
removeSelectedItemsCurrentParam(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
removeSelectedItemsCurrentParam.
removeSelectedItemsLaunchWorkflow(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
removeSelectedItemsLaunchWorkflow.
removeSequencerRun(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
removeSequencerRun.
removeStudy(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
removeStudy.
removeTags(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
removeTags(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
removeTagSpecIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
removeUsers(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
removeWorkflowRun(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
removeWorkflowRun.
removeWorkflowRunRunning(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
removeWorkflowRunRunning.
replace(String, String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.StringUtils
resolve all the FTL variables ${variable} in the string with the variables in maps
replace(String, Map<String, String>) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.StringUtils
replace.
report(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
report.
report(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageStatsProcessor
report.
report() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.MismatchConsequenceReportProcessor
report.
report(Object) - Method in interface net.sourceforge.seqware.queryengine.tools.iterators.processors.ProcessorInterface
report.
report(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
report.
report(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantStatsProcessor
report.
reportError(RecognitionException) - Method in class com.github.seqware.queryengine.kernel.SeqWareQueryLanguageLexerWrapper
reportError(RecognitionException) - Method in class com.github.seqware.queryengine.kernel.SeqWareQueryLanguageParserWrapper
reportException(ImportWorker) - Method in class com.github.seqware.queryengine.system.importers.FeatureImporter
reportException.
reportLaunch() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
Report an actual launch of a workflow for testing purpose
ReportTest - Class in net.sourceforge.seqware.pipeline.tools
ReportTest class.
ReportTest() - Constructor for class net.sourceforge.seqware.pipeline.tools.ReportTest
 
ReportTest.TestThread - Class in net.sourceforge.seqware.pipeline.tools
 
ReportTest.TestThread() - Constructor for class net.sourceforge.seqware.pipeline.tools.ReportTest.TestThread
 
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.CachedTagResource
represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.ConsequenceResource
represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.CoverageResource
represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.CoveragesResource
represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.FileResource
represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.GeneReportResource
represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.LiveTagResource
represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.MismatchesResource
represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.MismatchResource
represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.ProcessingResource
represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.TagResource
represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.TemplateResource
represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.VersionResource
represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.WorkflowResource
represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.WorkflowRunStatusResource
represent.
Requirement - Class in net.sourceforge.seqware.pipeline.workflowV2.model
 
Requirement() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
 
Requirement.Type - Enum in net.sourceforge.seqware.pipeline.workflowV2.model
enum of all Type
requireRegistration(HttpServletRequest, HttpServletResponse) - Static method in class net.sourceforge.solexatools.Security
requireRegistration.
requiresNewLauncher(Workflow) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility
 
requiresNewLauncher(String, String, String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility
 
requiresNewLauncher(OptionSet) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility
 
rerunWorkflowRun(Collection<String>, List<Integer>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
Returns true only if there are more files to run than have been run on any workflow so far, or if the filesToRun have different filepaths than those that have been run before.
resetCompletedChildren() - Method in class net.sourceforge.seqware.common.model.Processing
resetCompletedChildren.
resetRunningChildren() - Method in class net.sourceforge.seqware.common.model.Processing
resetRunningChildren.
RESOURCE_EXISTS - Static variable in class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
 
RESUBMITTED - Static variable in class net.sourceforge.seqware.common.metadata.Metadata
Constant RESUBMITTED="resubmitted"
ret - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
 
ret - Variable in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
ret - Variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
 
ret - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
RETURNEDHELPMSG - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant RETURNEDHELPMSG=110
ReturnValue - Class in net.sourceforge.seqware.common.module
Return values > 0 are errors that will cause the runner to exit.
ReturnValue() - Constructor for class net.sourceforge.seqware.common.module.ReturnValue
Constructor for ReturnValue.
ReturnValue(int) - Constructor for class net.sourceforge.seqware.common.module.ReturnValue
Constructor for ReturnValue.
ReturnValue(String, String, int) - Constructor for class net.sourceforge.seqware.common.module.ReturnValue
Constructor for ReturnValue.
returnValue - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
returnValue - Variable in class net.sourceforge.seqware.common.util.filetools.FileTools.LocalhostPair
 
ReturnValue.ExitStatus - Enum in net.sourceforge.seqware.common.module
 
ReturnValueList - Class in net.sourceforge.seqware.common.model.lists
ReturnValueList class.
ReturnValueList() - Constructor for class net.sourceforge.seqware.common.model.lists.ReturnValueList
Constructor for ReturnValueList.
RIGHTS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
root - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
RootSampleResource - Class in net.sourceforge.seqware.webservice.resources.tables
This resource should pull back only samples without parents
RootSampleResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.RootSampleResource
Constructor for RootSampleResource.
ROWKEY_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
ROWS_PER_PAGE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant ROWS_PER_PAGE="rp"
ROWS_PER_PAGE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant ROWS_PER_PAGE="rp"
RPNStack - Class in com.github.seqware.queryengine.kernel
A stack of arguments and operations in Reverse Polish Notation (RPN, http://en.wikipedia.org/wiki/Reverse_Polish_notation).
RPNStack(Object...) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack
Constructor for RPNStack.
RPNStack(List) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack
Constructor for RPNStack.
RPNStack.Constant - Class in com.github.seqware.queryengine.kernel
 
RPNStack.Constant(Object) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.Constant
 
RPNStack.FeatureAttribute - Class in com.github.seqware.queryengine.kernel
Represents attributes of features that are passed as parameter.
RPNStack.FeatureAttribute(String) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.FeatureAttribute
 
RPNStack.Operation - Enum in com.github.seqware.queryengine.kernel
Operations for combining query constraints.
RPNStack.Parameter - Class in com.github.seqware.queryengine.kernel
 
RPNStack.Parameter(String) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.Parameter
 
RPNStack.TagHierarchicalOccurrence - Class in com.github.seqware.queryengine.kernel
Represents tags whose occurrence is tested -- including the tags children!
RPNStack.TagHierarchicalOccurrence(String, String) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.TagHierarchicalOccurrence
 
RPNStack.TagOccurrence - Class in com.github.seqware.queryengine.kernel
Represents tags whose occurrence is probed.
RPNStack.TagOccurrence(String, String) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.TagOccurrence
 
RPNStack.TagValue - Class in com.github.seqware.queryengine.kernel
Represents tags whose value is retrieved
RPNStack.TagValue(String, String) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.TagValue
 
RPNStack.TagValuePresence - Class in com.github.seqware.queryengine.kernel
Represents tag/value pairs that should be present.
RPNStack.TagValuePresence(String, String, Tag.ValueType, Object) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.TagValuePresence
 
run() - Method in class com.github.seqware.queryengine.system.importers.workers.GFF3VariantImportWorker
run() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
run() - Method in class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker
run() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
run(String[]) - Method in class net.sourceforge.seqware.pipeline.runner.PluginRunner
run.
run(String[]) - Method in class net.sourceforge.seqware.pipeline.runner.Runner
run.
run() - Method in class net.sourceforge.seqware.pipeline.runner.Runner2
run.
run() - Method in class net.sourceforge.seqware.pipeline.tools.ReportTest.TestThread
 
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.BedFeatureImportWorker
run.
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.GFF3VariantImportWorker
run.
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
run.
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.PileupVariantImportWorker
run.
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.U87LargeDeletionVariantImportWorker
run.
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.U87TranslocationVariantImportWorker
run.
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.VCFVariantImportWorker
run.
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.VenterGenomeVariantImportWorker
run.
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.WatsonGenomeVariantImportWorker
run.
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.YanHuangGenomeVariantImportWorker
run.
run - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunSet
 
runattribute - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES
 
runattributes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
runCenter - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
runCommand(Map<String, String>, String) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
runCommand.
runCommand(String) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
runCommand.
runCommand(String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
runCommand.
runCommand(Map<String, String>, String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
A simple command runner that captures the return value of the program.
runDate - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
runFile - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
runInSessionCalculations() - Method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions
runInSessionCalculations.
runlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS
 
runlinks - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
runMain(String[]) - Static method in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper
Interface for mock-testing
runMain(String[]) - Static method in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
Interface for mock-testing
Runner - Class in net.sourceforge.seqware.pipeline.runner
Runner class.
Runner() - Constructor for class net.sourceforge.seqware.pipeline.runner.Runner
 
Runner.Keys - Interface in net.sourceforge.seqware.pipeline.runner
 
Runner2 - Class in net.sourceforge.seqware.pipeline.runner
This is a new Runner class that is designed (hopefuly) to replace the current Runner class.
Runner2() - Constructor for class net.sourceforge.seqware.pipeline.runner.Runner2
 
Runner2.ModuleConfig - Class in net.sourceforge.seqware.pipeline.runner
This class is used to configure the instantiating of a module
Runner2.ModuleConfig() - Constructor for class net.sourceforge.seqware.pipeline.runner.Runner2.ModuleConfig
 
RUNNERERR - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant RUNNERERR=91
RunnerParams - Class in net.sourceforge.seqware.pipeline.runner
This class is used to pass information from the Runner class to the Configuration class, which can instantiate the module and setup the bean.
RunnerParams() - Constructor for class net.sourceforge.seqware.pipeline.runner.RunnerParams
Constructor for RunnerParams.
RunnerParams.Bean - Interface in net.sourceforge.seqware.pipeline.runner
 
RUNNING - Static variable in class net.sourceforge.seqware.common.metadata.Metadata
Constant RUNNING="running"
RUNNING - Static variable in class net.sourceforge.seqware.common.model.WorkflowRun
Constant RUNNING="running"
RUNNING - Static variable in class net.sourceforge.seqware.pipeline.decider.Decider
Constant RUNNING="running"
RUNNING - Static variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
Constant RUNNING="running"
runPlugin(String) - Method in class com.github.seqware.queryengine.system.rest.resources.PluginResource
Retrieve resources.
runQuery(String, String, int) - Method in class com.github.seqware.queryengine.system.rest.resources.FeatureSetResource
Create new pluginrun event to create a query, monitor the query, and return a new feature set when ready.
runref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
 
RunSet - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunSet() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunSet
 
runStartTstmp - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
runStopTstmp - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
RUNTIMEEXCEPTION - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant RUNTIMEEXCEPTION=6
RunTools - Class in net.sourceforge.seqware.common.util.runtools
RunTools class.
RunTools() - Constructor for class net.sourceforge.seqware.common.util.runtools.RunTools
 
RunType - Class in net.sourceforge.seqware.queryengine.webservice.model
A Run contains the sequencing results from a particular run on a sequencing instrument.
RunType() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
RunType.DATABLOCK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.DATABLOCK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
 
RunType.DATABLOCK.FILES - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.DATABLOCK.FILES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES
 
RunType.DATABLOCK.FILES.FILE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.DATABLOCK.FILES.FILE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE
 
RunType.EXPERIMENTREF - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.EXPERIMENTREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF
 
RunType.RUNATTRIBUTES - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.RUNATTRIBUTES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES
 
RunType.RUNATTRIBUTES.RUNATTRIBUTE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.RUNATTRIBUTES.RUNATTRIBUTE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
 
RunType.RUNLINKS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.RUNLINKS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS
 
RunType.RUNLINKS.RUNLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.RUNLINKS.RUNLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK
 
RunType.RUNLINKS.RUNLINK.ENTREZLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.RUNLINKS.RUNLINK.ENTREZLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK
 
RunType.RUNLINKS.RUNLINK.URLLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
RunType.RUNLINKS.RUNLINK.URLLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK
 
runWorkflow(WorkflowInfo, String, String, boolean, String, ArrayList<String>, Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
runWorkflow.
runWorkflow(WorkflowInfo, String, String, boolean, String, ArrayList<String>, Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
runWorkflow.
runWorkflow(WorkflowInfo, String, String, boolean, String, ArrayList<String>, Registration) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowManager
runWorkflow.
RunWorkflowResource - Class in net.sourceforge.seqware.webservice.resources.queries
RunWorkflowResource class.
RunWorkflowResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.RunWorkflowResource
Constructor for RunWorkflowResource.

S

s3ConnectionTimeout - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
S3CreateFileURLs - Class in net.sourceforge.seqware.pipeline.modules.utilities
Purpose: This module simply lists files at the S3 URL you provide and creates temporary URLs that can be shared with others.
S3CreateFileURLs() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
S3DeleteFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities
Purpose: This module simply lists files at the S3 URL you provide.
S3DeleteFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
S3ListFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities
Purpose: This module simply lists files at the S3 URL you provide.
S3ListFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
s3MaxConnections - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
s3MaxErrorRetry - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
s3SocketTimeout - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
S3UploadDirectory - Class in net.sourceforge.seqware.pipeline.modules.utilities
Purpose: This module uses the Amazon API to recursively upload a directory to an S3 bucket.
S3UploadDirectory() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3UploadDirectory
 
Sample - Class in net.sourceforge.seqware.common.model
 
Sample() - Constructor for class net.sourceforge.seqware.common.model.Sample
Constructor for Sample.
sample - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleSet
 
SAMPLE_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant SAMPLE_ATTRIBUTES="Header.SAMPLE_ATTRIBUTES.getTitle()"
SAMPLE_CHILD - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant SAMPLE_CHILD="s_child"
SAMPLE_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant SAMPLE_NAME="Header.SAMPLE_NAME.getTitle()"
SAMPLE_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
Constant SAMPLE_PREFIX="sam_"
SAMPLE_SAMPLE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant SAMPLE_SAMPLE="s_sample"
SAMPLE_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant SAMPLE_SWA="Header.SAMPLE_SWA.getTitle()"
SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
Constant SAMPLE_SWID="sw"
SAMPLE_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant SAMPLE_TAG_PREFIX="Header.SAMPLE_TAG_PREFIX.getTitle()"
SampleAttribute - Class in net.sourceforge.seqware.common.model
SampleAttribute generated by hbm2java
SampleAttribute() - Constructor for class net.sourceforge.seqware.common.model.SampleAttribute
Constructor for SampleAttribute.
SampleAttribute(int, Sample, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleAttribute
Constructor for SampleAttribute.
SampleAttribute(int, Sample, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleAttribute
Constructor for SampleAttribute.
sampleattribute - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES
 
sampleAttributeAsDto(SampleAttribute) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos
sampleAttributeAsDto.
SampleAttributeDAO - Interface in net.sourceforge.seqware.common.dao
SampleAttributeDAO interface.
SampleAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
SampleAttributeDAOHibernate class.
SampleAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate
 
sampleattributes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
 
SampleController - Class in net.sourceforge.solexatools.webapp.controller
SampleController
SampleController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleController
Constructor for SampleController.
SampleController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleController
Constructor for SampleController.
SampleDAO - Interface in net.sourceforge.seqware.common.dao
SampleDAO interface.
SampleDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
SampleDAOHibernate class.
SampleDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
Constructor for SampleDAOHibernate.
sampledescriptor - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
 
SampleDetailsLineItem - Class in net.sourceforge.solexatools.webapp.metamodel
SampleDetailsLineItem class.
SampleDetailsLineItem(SequencerRun, Lane, IUS) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem
Constructor for SampleDetailsLineItem.
SampleDetailsWorkflowLineItems - Class in net.sourceforge.solexatools.webapp.metamodel
SampleDetailsWorkflowLineItems class.
SampleDetailsWorkflowLineItems(Sample) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
Constructor for SampleDetailsWorkflowLineItems.
SampleDetailsWorkflowLineItems(Processing) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems
Constructor for SampleDetailsWorkflowLineItems.
SampleHierarchies - Class in net.sourceforge.seqware.queryengine.webservice.model
 
SampleHierarchies() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchies
 
SampleHierarchy - Class in net.sourceforge.seqware.queryengine.webservice.model
 
SampleHierarchy() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy
 
SampleHierarchyResource - Class in net.sourceforge.seqware.webservice.resources.queries
 
SampleHierarchyResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SampleHierarchyResource
 
sampleId - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
 
sampleId - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
 
SampleIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries
SampleIdFilesResource class.
SampleIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SampleIdFilesResource
Constructor for SampleIdFilesResource.
SampleIDFilter - Class in net.sourceforge.seqware.webservice.resources.filters
SampleIDFilter class.
SampleIDFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.SampleIDFilter
 
SampleIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
SampleIDResource class.
SampleIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SampleIDResource
Constructor for SampleIDResource.
SampleLink - Class in net.sourceforge.seqware.common.model
SampleLink generated by hbm2java
SampleLink() - Constructor for class net.sourceforge.seqware.common.model.SampleLink
Constructor for SampleLink.
SampleLink(int, Sample, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleLink
Constructor for SampleLink.
SampleLink(int, Sample, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleLink
Constructor for SampleLink.
samplelink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS
 
SampleLinkDAO - Interface in net.sourceforge.seqware.common.dao
SampleLinkDAO interface.
SampleLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
SampleLinkDAOHibernate class.
SampleLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate
 
samplelinks - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
 
SampleList - Class in net.sourceforge.seqware.common.model.lists
SampleList class.
SampleList() - Constructor for class net.sourceforge.seqware.common.model.lists.SampleList
Constructor for SampleList.
samplename - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
 
samplepoolref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
 
sampleRef - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
 
sampleref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
 
sampleRef - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
 
SampleReportDAO - Interface in net.sourceforge.seqware.common.dao
SampleReportDAO interface.
SampleReportDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
SampleReportDAOHibernate class.
SampleReportDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
 
SampleReportRow - Class in net.sourceforge.seqware.common.model
SampleReportRow class.
SampleReportRow() - Constructor for class net.sourceforge.seqware.common.model.SampleReportRow
 
SampleReportService - Interface in net.sourceforge.seqware.common.business
SampleReportService interface.
SampleReportServiceImpl - Class in net.sourceforge.seqware.common.business.impl
SampleReportServiceImpl class.
SampleReportServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
 
SampleResource - Class in net.sourceforge.seqware.webservice.resources.tables
SampleResource class.
SampleResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SampleResource
Constructor for SampleResource.
SampleSearch - Class in net.sourceforge.seqware.common.model
A search for samples that match a given list of attributes.
SampleSearch() - Constructor for class net.sourceforge.seqware.common.model.SampleSearch
 
SampleSearchAttribute - Class in net.sourceforge.seqware.common.model
Attributes that are part of a sample search.
SampleSearchAttribute() - Constructor for class net.sourceforge.seqware.common.model.SampleSearchAttribute
 
SampleSearchDAO - Interface in net.sourceforge.seqware.common.dao
SampleSearchDAO interface.
SampleSearchDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
SampleSearchDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleSearchDAOHibernate
 
SampleSearchDto - Class in net.sourceforge.seqware.webservice.dto
 
SampleSearchDto() - Constructor for class net.sourceforge.seqware.webservice.dto.SampleSearchDto
 
SampleSearchService - Interface in net.sourceforge.seqware.common.business
SampleSearchService interface.
SampleSearchServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
SampleSearchServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SampleSearchServiceImpl
 
SampleService - Interface in net.sourceforge.seqware.common.business
SampleService interface.
SampleServiceImpl - Class in net.sourceforge.seqware.common.business.impl
SampleServiceImpl class.
SampleServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
Constructor for SampleServiceImpl.
SampleSet - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleSet() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleSet
 
SampleSetupController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
SampleSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleSetupController
Constructor for SampleSetupController.
SampleType - Class in net.sourceforge.seqware.queryengine.webservice.model
A Sample defines an isolate of sequenceable material upon which sequencing experiments can be based.
SampleType() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType
 
SampleType.MEMBERS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleType.MEMBERS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS
 
SampleType.MEMBERS.MEMBER - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleType.MEMBERS.MEMBER() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
 
SampleType.SAMPLEATTRIBUTES - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleType.SAMPLEATTRIBUTES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES
 
SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
 
SampleType.SAMPLELINKS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleType.SAMPLELINKS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS
 
SampleType.SAMPLELINKS.SAMPLELINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleType.SAMPLELINKS.SAMPLELINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK
 
SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
 
SampleType.SAMPLELINKS.SAMPLELINK.URLLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleType.SAMPLELINKS.SAMPLELINK.URLLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
 
SampleType.SAMPLENAME - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SampleType.SAMPLENAME() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
 
SampleValidator - Class in net.sourceforge.solexatools.validation
SampleValidator class.
SampleValidator() - Constructor for class net.sourceforge.solexatools.validation.SampleValidator
Constructor for SampleValidator.
SampleWorkflowRunsController - Class in net.sourceforge.solexatools.webapp.controller
SampleWorkflowRunsController class.
SampleWorkflowRunsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
 
saveAscInSession(HttpServletRequest, String) - Static method in class net.sourceforge.solexatools.util.ControllerUtil
saveAscInSession.
saveAscInSession(HttpServletRequest, String) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
saveAscInSession.
saveFile(MultipartFile, String, Registration) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
saveFile.
saveFile(MultipartFile, String, Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
saveFile.
saveFileForIus(int, int, FileMetadata, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
saveFileForIus.
saveFileForIus(int, int, FileMetadata, int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
saveFileForIus.
saveFileForIus(int, int, FileMetadata, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
saveFileForIus.
saveFileForIus(int, int, FileMetadata, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
saveFileForIus.
SaveOpenNodeController - Class in net.sourceforge.solexatools.webapp.controller
SaveOpenNodeController class.
SaveOpenNodeController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
Constructor for SaveOpenNodeController.
saveSelectedWorkflowParamValue(HttpServletRequest, Integer, String) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
saveSelectedWorkflowParamValue.
scan(T) - Method in interface com.github.seqware.queryengine.plugins.ScanPlugin
Scanner implementation that processes atoms and aggregates results in a new set.
ScanPlugin<T extends Atom,S> - Interface in com.github.seqware.queryengine.plugins
An abstracted map-reduce interface.
SCHEDULE - Static variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
 
scheduleInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
scheduleInstalledBundle.
scheduleInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>, String) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
This method just needs a sw_accession value from the workflow table and an ini file(s) in order to schedule a workflow.
scheduleInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.WorkflowEngine
scheduleInstalledBundle.
scheduleWorkflowRun(int, String, String, String, String, String, String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
scheduleWorkflowRun.
schema - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
 
schema - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
 
score - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
SCORE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
SEARCH_CASE_SENSITIVE - Static variable in class net.sourceforge.solexatools.webapp.controller.SearchController
Constant SEARCH_CASE_SENSITIVE="search.checked"
SearchController - Class in net.sourceforge.solexatools.webapp.controller
SearchController class.
SearchController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SearchController
Constructor for SearchController.
SearchResultsController - Class in net.sourceforge.solexatools.webapp.controller
SearchResultsController class.
SearchResultsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SearchResultsController
 
SearchResultsListController - Class in net.sourceforge.solexatools.webapp.controller
SearchResultsListController class.
SearchResultsListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
Constructor for SearchResultsListController.
SECONDARY_INDEX - Static variable in class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker
Constant SECONDARY_INDEX="sIndex.out"
SECONDARY_INDEX_HACK - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
Constant SECONDARY_INDEX_HACK=false
SECONDARY_INDEX_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
Constant SECONDARY_INDEX_PARAM='x'
SecondaryCursorIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators
SecondaryCursorIterator class.
SecondaryCursorIterator(SecondaryCursor, TupleBinding, boolean) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator
Used to iterate over an entire secondary table with or without duplicates reported
SecondaryCursorIterator(SecondaryCursor, DatabaseEntry, TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator
Used to search the secondary table with only duplicates reported back
secretKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
secretKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
secretKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
sector - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
 
Security - Class in net.sourceforge.solexatools
Security class.
Security() - Constructor for class net.sourceforge.solexatools.Security
 
SELECTED_FILES - Static variable in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
Constant SELECTED_FILES="selectedLaunchFiles"
SELECTED_NODES - Static variable in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
Constant SELECTED_NODES="launchSelectedNodes"
SELECTED_VALUES - Static variable in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
Constant SELECTED_VALUES="selectedWorkflowParamValueId"
selectExperimentNode(List<String>, Study) - Static method in class net.sourceforge.solexatools.util.BulkUtil
selectExperimentNode.
SelectInputController - Class in net.sourceforge.solexatools.webapp.controller
SelectInputController class.
SelectInputController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SelectInputController
Constructor for SelectInputController.
SelectInputController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SelectInputController
Constructor for SelectInputController.
SelectInputListController - Class in net.sourceforge.solexatools.webapp.controller
SelectInputListController class.
SelectInputListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SelectInputListController
Constructor for SelectInputListController.
selectIUSNode(List<String>, Sample) - Static method in class net.sourceforge.solexatools.util.BulkUtil
selectIUSNode.
selectProcessingNode(List<String>, WorkflowRun) - Static method in class net.sourceforge.solexatools.util.BulkUtil
selectProcessingNode.
selectProcessingNode(List<String>, Processing) - Static method in class net.sourceforge.solexatools.util.BulkUtil
selectProcessingNode.
selectProcessingNode(List<String>, Lane) - Static method in class net.sourceforge.solexatools.util.BulkUtil
selectProcessingNode.
selectProcessingNode(List<String>, IUS) - Static method in class net.sourceforge.solexatools.util.BulkUtil
selectProcessingNode.
selectSampleNode(List<String>, Experiment) - Static method in class net.sourceforge.solexatools.util.BulkUtil
selectSampleNode.
selectStudyNode(List<String>, List<Study>) - Static method in class net.sourceforge.solexatools.util.BulkUtil
selectStudyNode.
selectWorkflowRunNode(List<String>, List<WorkflowRun>) - Static method in class net.sourceforge.solexatools.util.BulkUtil
selectWorkflowRunNode.
separateFiles(List<ReturnValue>, String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
SEPARATOR - Static variable in class com.github.seqware.queryengine.backInterfaces.StorageInterface
Constant SEPARATOR="."
SEPARATOR - Static variable in class com.github.seqware.queryengine.model.Tag
Constant SEPARATOR="::"
SEPARATOR - Static variable in class net.sourceforge.solexatools.webapp.controller.ChangeNumberPopupPageController
Constant SEPARATOR="java.io.File.separator"
SEPARATOR - Static variable in class net.sourceforge.solexatools.webapp.controller.DeleteLoadedIndexPageController
Constant SEPARATOR="java.io.File.separator"
SEQ_RUN_ID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant SEQ_RUN_ID="seq_run_id"
SEQUENCER_RUN_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant SEQUENCER_RUN_ATTRIBUTES="Header.SEQUENCER_RUN_ATTRIBUTES.getTitl"{trunked}
SEQUENCER_RUN_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant SEQUENCER_RUN_NAME="Header.SEQUENCER_RUN_NAME.getTitle()"
SEQUENCER_RUN_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant SEQUENCER_RUN_SWA="Header.SEQUENCER_RUN_SWA.getTitle()"
SEQUENCER_RUN_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant SEQUENCER_RUN_TAG_PREFIX="Header.SEQUENCER_RUN_TAG_PREFIX.getTitl"{trunked}
SEQUENCER_VIEW - Static variable in class net.sourceforge.solexatools.util.Constant
Constant SEQUENCER_VIEW="redirect:/sequencerRunList.htm"
SequencerRun - Class in net.sourceforge.seqware.common.model
 
SequencerRun() - Constructor for class net.sourceforge.seqware.common.model.SequencerRun
Constructor for SequencerRun.
SequencerRunAttribute - Class in net.sourceforge.seqware.common.model
SequencerRunAttribute generated by Morgan Taschuk
SequencerRunAttribute() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunAttribute
Constructor for SequencerRunAttribute.
SequencerRunAttribute(int, SequencerRunWizardDTO) - Constructor for class net.sourceforge.seqware.common.model.SequencerRunAttribute
Constructor for SequencerRunAttribute.
SequencerRunAttribute(int, SequencerRunWizardDTO, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.SequencerRunAttribute
Constructor for SequencerRunAttribute.
SequencerRunController - Class in net.sourceforge.solexatools.webapp.controller
SequencerRunController
SequencerRunController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunController
Constructor for SequencerRunController.
SequencerRunController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunController
Constructor for SequencerRunController.
SequencerRunControllerDTO - Class in net.sourceforge.solexatools.webapp.controller
SequencerRunController
SequencerRunControllerDTO() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
Constructor for SequencerRunControllerDTO.
SequencerRunControllerDTO(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
Constructor for SequencerRunControllerDTO.
SequencerRunDAO - Interface in net.sourceforge.seqware.common.dao
SequencerRunDAO interface.
SequencerRunDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
SequencerRunDAOHibernate class.
SequencerRunDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
Constructor for SequencerRunDAOHibernate.
SequencerRunDTO - Class in net.sourceforge.seqware.common.model
 
SequencerRunDTO() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunDTO
Constructor for SequencerRunDTO.
SequencerRunHtmlUtil - Class in net.sourceforge.solexatools.util
SequencerRunHtmlUtil class.
SequencerRunHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
 
SequencerRunIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries
SequencerRunIdFilesResource class.
SequencerRunIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SequencerRunIdFilesResource
Constructor for SequencerRunIdFilesResource.
SequencerRunIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
SequencerRunIDResource class.
SequencerRunIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SequencerRunIDResource
Constructor for SequencerRunIDResource.
SequencerRunList - Class in net.sourceforge.seqware.common.model.lists
SequencerRunList class.
SequencerRunList() - Constructor for class net.sourceforge.seqware.common.model.lists.SequencerRunList
Constructor for SequencerRunList.
SequencerRunListController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
SequencerRunListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunListController
Constructor for SequencerRunListController.
SequencerRunListDetailsController - Class in net.sourceforge.solexatools.webapp.controller
SequencerRunListDetailsController class.
SequencerRunListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
Constructor for SequencerRunListDetailsController.
SequencerRunReport - Class in net.sourceforge.seqware.common.hibernate
SequencerRunReport class.
SequencerRunReport() - Constructor for class net.sourceforge.seqware.common.hibernate.SequencerRunReport
 
SequencerRunReport.Row - Class in net.sourceforge.seqware.common.hibernate
 
SequencerRunReport.Row(Date, String, String, String, String, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
SequencerRunReporter - Class in net.sourceforge.seqware.pipeline.plugins
SequencerRunReporter class.
SequencerRunReporter() - Constructor for class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter
Constructor for SequencerRunReporter.
SequencerRunReportId - Class in net.sourceforge.seqware.common.model
SequencerRunReportId class.
SequencerRunReportId() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunReportId
 
SequencerRunReportResource - Class in net.sourceforge.seqware.webservice.resources.queries
SequencerRunReportResource class.
SequencerRunReportResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SequencerRunReportResource
Constructor for SequencerRunReportResource.
SequencerRunReportSetupController - Class in net.sourceforge.solexatools.webapp.controller
 
SequencerRunReportSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunReportSetupController
 
SequencerRunReportTableController - Class in net.sourceforge.solexatools.webapp.controller
 
SequencerRunReportTableController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
 
SequencerRunResource - Class in net.sourceforge.seqware.webservice.resources.tables
SequencerRunResource class.
SequencerRunResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SequencerRunResource
Constructor for SequencerRunResource.
SequencerRunService - Interface in net.sourceforge.seqware.common.business
SequencerRunService interface.
SequencerRunServiceImpl - Class in net.sourceforge.seqware.common.business.impl
SequencerRunServiceImpl class.
SequencerRunServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
Constructor for SequencerRunServiceImpl.
SequencerRunSetupController - Class in net.sourceforge.solexatools.webapp.controller
SequencingRunSetupController
SequencerRunSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController
Constructor for SequencerRunSetupController.
SequencerRunSetupControllerDTO - Class in net.sourceforge.solexatools.webapp.controller
SequencingRunSetupController
SequencerRunSetupControllerDTO() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO
Constructor for SequencerRunSetupControllerDTO.
SequencerRunValidator - Class in net.sourceforge.solexatools.validation
SequencerRunValidator class.
SequencerRunValidator() - Constructor for class net.sourceforge.solexatools.validation.SequencerRunValidator
Constructor for SequencerRunValidator.
SequencerRunWizardController - Class in net.sourceforge.solexatools.webapp.controller
SequencerRunWizardController class.
SequencerRunWizardController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Constructor for SequencerRunWizardController.
SequencerRunWizardController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Constructor for SequencerRunWizardController.
SequencerRunWizardDTO - Class in net.sourceforge.seqware.common.model
SequencerRunWizardDTO class.
SequencerRunWizardDTO() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
Constructor for SequencerRunWizardDTO.
SequencerRunWizardSetupController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
SequencerRunWizardSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
Constructor for SequencerRunWizardSetupController.
SequencerRunWizardValidator - Class in net.sourceforge.solexatools.validation
SequencerRunWizardValidator class.
SequencerRunWizardValidator() - Constructor for class net.sourceforge.solexatools.validation.SequencerRunWizardValidator
Constructor for SequencerRunWizardValidator.
sequencespace - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS
 
sequencingprotocol - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
 
SEQWARE_SETTINGS_PROPERTY - Static variable in class net.sourceforge.seqware.common.util.configtools.ConfigTools
Constant SEQWARE_SETTINGS_PROPERTY="SEQWARE_SETTINGS"
SeqwareAccessionIDResource - Class in net.sourceforge.seqware.webservice.resources
SeqwareAccessionIDResource class.
SeqwareAccessionIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
 
SeqwareAccessionResource - Class in net.sourceforge.seqware.webservice.resources
SeqwareAccessionResource class.
SeqwareAccessionResource() - Constructor for class net.sourceforge.seqware.webservice.resources.SeqwareAccessionResource
 
SeqWareBase - Class in net.sourceforge.seqware.queryengine.backend.util
SeqWareBase class.
SeqWareBase() - Constructor for class net.sourceforge.seqware.queryengine.backend.util.SeqWareBase
 
SeqWareCursor - Class in net.sourceforge.seqware.queryengine.backend.util
SeqWareCursor class.
SeqWareCursor() - Constructor for class net.sourceforge.seqware.queryengine.backend.util.SeqWareCursor
 
SeqwareException - Exception in net.sourceforge.seqware.common.err
Created by IntelliJ IDEA.
SeqwareException() - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException
Constructor for SeqwareException.
SeqwareException(String) - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException
Constructor for SeqwareException.
SeqwareException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException
Constructor for SeqwareException.
SeqwareException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException
Constructor for SeqwareException.
SeqWareException - Exception in net.sourceforge.seqware.queryengine.backend.util
SeqWareException class.
SeqWareException() - Constructor for exception net.sourceforge.seqware.queryengine.backend.util.SeqWareException
Constructor for SeqWareException.
SeqWareException(String) - Constructor for exception net.sourceforge.seqware.queryengine.backend.util.SeqWareException
Constructor for SeqWareException.
SeqWareException(Throwable) - Constructor for exception net.sourceforge.seqware.queryengine.backend.util.SeqWareException
Constructor for SeqWareException.
SeqWareException(String, Throwable) - Constructor for exception net.sourceforge.seqware.queryengine.backend.util.SeqWareException
Constructor for SeqWareException.
SeqwareExitCode - Class in net.sourceforge.seqware.common.err
Created by IntelliJ IDEA.
SeqwareExitCode() - Constructor for class net.sourceforge.seqware.common.err.SeqwareExitCode
 
SeqWareIterable<T> - Interface in com.github.seqware.queryengine.util
All SeqWare iterable collections should be easily countable too
SeqWareIterator<T> - Class in com.github.seqware.queryengine.util
Iterator implementation that deals with database iterators that require explicit closing.
SeqWareIterator() - Constructor for class com.github.seqware.queryengine.util.SeqWareIterator
 
SeqWareIterator - Interface in net.sourceforge.seqware.queryengine.backend.util
SeqWareIterator interface.
SeqWareQueryLanguageLexer - Class in com.github.seqware.queryengine.kernel.output
SeqWareQueryLanguageLexer class.
SeqWareQueryLanguageLexer() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constructor for SeqWareQueryLanguageLexer.
SeqWareQueryLanguageLexer(CharStream) - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constructor for SeqWareQueryLanguageLexer.
SeqWareQueryLanguageLexer(CharStream, RecognizerSharedState) - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constructor for SeqWareQueryLanguageLexer.
SeqWareQueryLanguageLexerWrapper - Class in com.github.seqware.queryengine.kernel
SeqWareQueryLanguageLexerWrapper class.
SeqWareQueryLanguageLexerWrapper(CharStream) - Constructor for class com.github.seqware.queryengine.kernel.SeqWareQueryLanguageLexerWrapper
Constructor for SeqWareQueryLanguageLexerWrapper.
SeqWareQueryLanguageParser - Class in com.github.seqware.queryengine.kernel.output
SeqWareQueryLanguageParser class.
SeqWareQueryLanguageParser(TokenStream) - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constructor for SeqWareQueryLanguageParser.
SeqWareQueryLanguageParser(TokenStream, RecognizerSharedState) - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constructor for SeqWareQueryLanguageParser.
SeqWareQueryLanguageParser.comment_return - Class in com.github.seqware.queryengine.kernel.output
 
SeqWareQueryLanguageParser.comment_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.comment_return
 
SeqWareQueryLanguageParser.comparison_return - Class in com.github.seqware.queryengine.kernel.output
 
SeqWareQueryLanguageParser.comparison_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.comparison_return
 
SeqWareQueryLanguageParser.constant_return - Class in com.github.seqware.queryengine.kernel.output
 
SeqWareQueryLanguageParser.constant_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.constant_return
 
SeqWareQueryLanguageParser.constraint_return - Class in com.github.seqware.queryengine.kernel.output
 
SeqWareQueryLanguageParser.constraint_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.constraint_return
 
SeqWareQueryLanguageParser.high_precedence_constraint_return - Class in com.github.seqware.queryengine.kernel.output
 
SeqWareQueryLanguageParser.high_precedence_constraint_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.high_precedence_constraint_return
 
SeqWareQueryLanguageParser.identifier_return - Class in com.github.seqware.queryengine.kernel.output
 
SeqWareQueryLanguageParser.identifier_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.identifier_return
 
SeqWareQueryLanguageParser.key_value_function_return - Class in com.github.seqware.queryengine.kernel.output
 
SeqWareQueryLanguageParser.key_value_function_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.key_value_function_return
 
SeqWareQueryLanguageParser.literal_return - Class in com.github.seqware.queryengine.kernel.output
 
SeqWareQueryLanguageParser.literal_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.literal_return
 
SeqWareQueryLanguageParser.low_precedence_constraint_return - Class in com.github.seqware.queryengine.kernel.output
 
SeqWareQueryLanguageParser.low_precedence_constraint_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.low_precedence_constraint_return
 
SeqWareQueryLanguageParser.nested_constraint_return - Class in com.github.seqware.queryengine.kernel.output
 
SeqWareQueryLanguageParser.nested_constraint_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.nested_constraint_return
 
SeqWareQueryLanguageParser.query_return - Class in com.github.seqware.queryengine.kernel.output
 
SeqWareQueryLanguageParser.query_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.query_return
 
SeqWareQueryLanguageParser.three_param_predicate_return - Class in com.github.seqware.queryengine.kernel.output
 
SeqWareQueryLanguageParser.three_param_predicate_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.three_param_predicate_return
 
SeqWareQueryLanguageParser.two_param_predicate_return - Class in com.github.seqware.queryengine.kernel.output
 
SeqWareQueryLanguageParser.two_param_predicate_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.two_param_predicate_return
 
SeqWareQueryLanguageParserWrapper - Class in com.github.seqware.queryengine.kernel
SeqWareQueryLanguageParserWrapper class.
SeqWareQueryLanguageParserWrapper(TokenStream) - Constructor for class com.github.seqware.queryengine.kernel.SeqWareQueryLanguageParserWrapper
Constructor for SeqWareQueryLanguageParserWrapper.
SeqWareSettings - Class in net.sourceforge.seqware.queryengine.backend.util
SeqWareSettings class.
SeqWareSettings() - Constructor for class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
 
SeqWareVerifier - Class in net.sourceforge.seqware.queryengine.webservice.security
SeqWareVerifier class.
SeqWareVerifier() - Constructor for class net.sourceforge.seqware.queryengine.webservice.security.SeqWareVerifier
 
SeqWareWebServiceApplication - Class in net.sourceforge.seqware.queryengine.webservice.controller
SeqWareWebServiceApplication class.
SeqWareWebServiceApplication() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication
 
SeqWareWebServiceApplication.OptionalSlashRedirect - Class in net.sourceforge.seqware.queryengine.webservice.controller
http://restlet-discuss.1400322.n2.nabble.com/Proper-handling-of-at-the-end-of-the-requested-URI-td5819896.html
SeqWareWebServiceApplication.OptionalSlashRedirect(Context) - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication.OptionalSlashRedirect
 
SeqWareWebServiceApplication.OptionalSlashRedirect() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication.OptionalSlashRedirect
 
SeqWareWebServiceApplicationVersion - Class in net.sourceforge.seqware.queryengine.webservice.controller
SeqWareWebServiceApplicationVersion class.
SeqWareWebServiceApplicationVersion() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion
 
SeqWareWebServiceApplicationVersion.OptionalSlashRedirect - Class in net.sourceforge.seqware.queryengine.webservice.controller
http://restlet-discuss.1400322.n2.nabble.com/Proper-handling-of-at-the-end-of-the-requested-URI-td5819896.html
SeqWareWebServiceApplicationVersion.OptionalSlashRedirect(Context) - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion.OptionalSlashRedirect
 
SeqWareWebServiceApplicationVersion.OptionalSlashRedirect() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion.OptionalSlashRedirect
 
SeqWareWebServiceMain - Class in net.sourceforge.seqware.queryengine.webservice.controller
SeqWareWebServiceMain class.
SERIALIZATIONCONSTANT_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
SERIALIZATIONCONSTANT_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
SerializationInterface - Interface in com.github.seqware.queryengine.backInterfaces
This simply extracts the serialization of bytes[] to atoms and vice versa.
serialize(Atom) - Method in interface com.github.seqware.queryengine.backInterfaces.SerializationInterface
Given an atom, get back an array of bytes
serialize(Atom) - Method in class com.github.seqware.queryengine.impl.ApacheSerialization
Given an atom, get back an array of bytes
serialize(Atom) - Method in class com.github.seqware.queryengine.impl.KryoSerialization
Given an atom, get back an array of bytes
serialize(Atom) - Method in class com.github.seqware.queryengine.impl.ProtobufSerialization
Given an atom, get back an array of bytes
serializeAtomsToTarget(T...) - Method in class com.github.seqware.queryengine.backInterfaces.StorageInterface
Generically serialize a batch of Atoms, all of the same class This method is also responsible for ensuring that the atom's backendTimestamp is populated
serializeAtomsToTarget(T...) - Method in class com.github.seqware.queryengine.impl.HBaseStorage
Generically serialize a batch of Atoms, all of the same class This method is also responsible for ensuring that the atom's backendTimestamp is populated
serializeAtomsToTarget(T...) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
Generically serialize a batch of Atoms, all of the same class This method is also responsible for ensuring that the atom's backendTimestamp is populated
serializeAtomsToTarget(Atom...) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
Generically serialize a batch of Atoms, all of the same class This method is also responsible for ensuring that the atom's backendTimestamp is populated
serializeAtomToTarget(Atom) - Method in class com.github.seqware.queryengine.backInterfaces.StorageInterface
Generically serialize an Atom into the interface This method is also responsible for ensuring that the atom's backendTimestamp is populated
serializeAtomToTarget(Atom) - Method in class com.github.seqware.queryengine.impl.HBaseStorage
Generically serialize an Atom into the interface This method is also responsible for ensuring that the atom's backendTimestamp is populated
serializeAtomToTarget(Atom) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage
Generically serialize an Atom into the interface This method is also responsible for ensuring that the atom's backendTimestamp is populated
serializeAtomToTarget(Atom) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage
Generically serialize an Atom into the interface This method is also responsible for ensuring that the atom's backendTimestamp is populated
serializeParametersToString(Object[], PluginInterface, byte[], byte[]) - Static method in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner
 
serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob
 
serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp
 
serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Adag
Adag object serialize to element and all its sub objects serialize to sub element
serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn
serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
 
set - Variable in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
 
set(T) - Method in class com.github.seqware.queryengine.util.LazyReference
Set the lazy reference of the object with an actual object.
setABISOLID(ExperimentType.PLATFORM.ABISOLID) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
Sets the value of the abisolid property.
setAbstractStr(String) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field abstractStr.
setABUNDANCEMEASUREMENT(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Sets the value of the abundancemeasurement property.
setAccession(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field accession.
setAccession(String) - Method in class net.sourceforge.seqware.common.model.Organism
Setter for the field accession.
setAccession(String) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field accession.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the accession property.
setAcl(QueryEngine.ACLPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
setAcl(QueryEngine.ACLPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
setACTIONS(SubmissionType.ACTIONS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the actions property.
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
Setter for the field active.
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareFile
Setter for the field active.
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareLane
Setter for the field active.
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
Setter for the field active.
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareSample
Setter for the field active.
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareStudy
Setter for the field active.
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
Setter for the field active.
setAdapters(String) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field adapters.
setAdapterSpec(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
Setter for the field adapterSpec.
setADAPTERSPEC(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
Sets the value of the adapterspec property.
setADD(SubmissionType.ACTIONS.ACTION.ADD) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Sets the value of the add property.
setAddedSurcharge(Double) - Method in class net.sourceforge.seqware.common.model.Expense
Setter for the field addedSurcharge.
setAdditionalAttribute(String, Feature.AdditionalAttributeType) - Method in class com.github.seqware.queryengine.model.Feature
Sets an additional attribute not covered by GVF.
setAdhoctagset(SGID) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Setter for the field adhoctagset.
setAgent(String) - Method in class net.sourceforge.seqware.common.model.Expense
Setter for the field agent.
setAlgo(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
set the job algorithm
setAlgorithm(String) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field algorithm.
setAlgorithm(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
Setter for the field algorithm.
setAlgorithm(String) - Method in class net.sourceforge.seqware.pipeline.module.Module
Setter for the field algorithm.
setAlias(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field alias.
setAlias(String) - Method in class net.sourceforge.seqware.common.model.IUS
Setter for the field alias.
setAlias(String) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field alias.
setAlias(String) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field alias.
setAlias(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the alias property.
setAlias(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the alias property.
setAlias(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the alias property.
setAlias(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Sets the value of the alias property.
setAlias(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Sets the value of the alias property.
setAlias(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the alias property.
setAlign(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
setAllItems(String) - Method in class net.sourceforge.solexatools.util.PageInfo
Setter for the field allItems.
setANALYSISATTRIBUTES(AnalysisType.ANALYSISATTRIBUTES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the analysisattributes property.
setAnalysisCenter(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the analysisCenter property.
setANALYSISFILES(AnalysisType.ANALYSISFILES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the analysisfiles property.
setANALYSISLINKS(AnalysisType.ANALYSISLINKS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the analysislinks property.
setAnalysisPluginACL(ACL, AnalysisPlugin) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
setAnalysisPluginACL.
setAnalysisSetACL(ACL, AnalysisSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
setAnalysisSetACL.
setANALYSISTYPE(AnalysisType.ANALYSISTYPE) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the analysistype property.
setAnonymizedName(String) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field anonymizedName.
setANONYMIZEDNAME(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
Sets the value of the anonymizedname property.
setApplicationContext(ApplicationContext) - Method in class net.sourceforge.seqware.pipeline.runner.Runner2
setApplicationContext.
setArch(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
 
setArgs(String[]) - Method in class net.sourceforge.seqware.pipeline.tools.ReportTest.TestThread
 
setArguments(List<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
 
setAsText(String) - Method in class net.sourceforge.solexatools.validation.CustomIntegerEditor
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
setAtom(QESupporting.FeatureAtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setAtom(QESupporting.FeatureAtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setAtom(Atom) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager.AtomStatePair
 
setAttribute(String, String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
setAttribute.
setAttributes(Map<String, String>) - Method in class net.sourceforge.seqware.common.module.ReturnValue
Setter for the field attributes.
setAttributes(Set<AttributeDto>) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Setter for the field attributes.
setAttributes(Set<AttributeDto>) - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto
Setter for the field attributes.
setBackendTimestamp(Date) - Method in class com.github.seqware.queryengine.util.SGID
Setter for the field backendTimestamp.
setBarcode(String) - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Set the value of barcode
setBarcode(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Setter for the field barcode.
setBarcodeSeqence(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
Sets the value of the barcodeSeqence property.
setBaseCaller(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field baseCaller.
setBASECALLER(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS
Sets the value of the basecaller property.
setBASECALLS(ExperimentType.PROCESSING.BASECALLS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING
Sets the value of the basecalls property.
setBaseCoord(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Setter for the field baseCoord.
setBASECOORD(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Sets the value of the basecoord property.
setBaseDir(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Setter for the field baseDir.
setBaseIniFile(String) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field baseIniFile.
setBaseQualities(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field baseQualities.
setBatch_size(int) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Setter for the field batch_size.
setBinSize(int) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Setter for the field binSize.
setBinSize(int) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Setter for the field binSize.
setBlockCount(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Setter for the field blockCount.
setBlockSizes(int[]) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Setter for the field blockSizes.
setBlockStarts(int[]) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Setter for the field blockStarts.
setBrokerName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the brokerName property.
setCacheSize(long) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field cacheSize.
setCalledBase(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field calledBase.
setCalledBaseCount(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field calledBaseCount.
setCalledBaseCountForward(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field calledBaseCountForward.
setCalledBaseCountReverse(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field calledBaseCountReverse.
setCallOne(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field callOne.
setCallTwo(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field callTwo.
setCascade(boolean) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
setCell(List<String>) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.Cells
 
setCenterName(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field centerName.
setCenterName(String) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field centerName.
setCenterName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the centerName property.
setCENTERNAME(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Sets the value of the centername property.
setCenterName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the centerName property.
setCenterProjectName(String) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field centerProjectName.
setCENTERPROJECTNAME(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Sets the value of the centerprojectname property.
setChecksum(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
Sets the value of the checksum property.
setChecksumMethod(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
Sets the value of the checksumMethod property.
setChildren(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field children.
setChildren(Set<Sample>) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field children.
setChildrenUrls(Set<String>) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Setter for the field childrenUrls.
setChildSample(Sample) - Method in class net.sourceforge.seqware.common.model.FileReportRow
Setter for the field childSample.
setChildSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
Setter for the field childSample.
setChildSample(Sample) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
Setter for the field childSample.
setChildSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
Setter for the field childSample.
setChildSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Setter for the field childSample.
setClassesDir(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Setter for the field classesDir.
setClientNotes(String) - Method in class net.sourceforge.seqware.common.model.Invoice
Setter for the field clientNotes.
setCode(String) - Method in class net.sourceforge.seqware.common.model.Organism
Setter for the field code.
setCode(String) - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto
Setter for the field code.
setCodingStart(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Setter for the field codingStart.
setCodingStop(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Setter for the field codingStop.
setColorMatrix(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field colorMatrix.
setColorMatrix(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field colorMatrix.
setCOLORMATRIX(ExperimentType.PLATFORM.ABISOLID.COLORMATRIX) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
Sets the value of the colormatrix property.
setColorMatrixCode(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field colorMatrixCode.
setColorMatrixCode(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field colorMatrixCode.
setCOLORMATRIXCODE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
Sets the value of the colormatrixcode property.
setCommand(String) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field command.
setCommand(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field command.
setCommand(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Setter for the field command.
setCommand(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
setCommand(String) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
set the job command
setCOMMONNAME(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
Sets the value of the commonname property.
setCompleted(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Setter for the field completed.
setCompressed(boolean) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Setter for the field compressed.
setCompressed(boolean) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Setter for the field compressed.
setCompute(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setComputeReq(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Setter for the field computeReq.
setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.decider.Decider
Let's you set the config this object should use.
setConfig(Map<String, String>) - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Let's you set the config this object should use.
setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
Let's you set the config this object should use.
setConfig(Map<String, String>) - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Let's you set the config this object should use.
setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
Let's you set the config this object should use.
setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
Let's you set the config this object should use.
setConfigPath(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Setter for the field configPath.
setConfigs(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
set the key-value properties for workflow
setConfirmEmailAddress(String) - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
Setter for the field confirmEmailAddress.
setConfirmPassword(String) - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
Setter for the field confirmPassword.
setConnectionString(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field connectionString.
setConsensusAveSeqQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field consensusAveSeqQuality.
setConsensusBase(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field consensusBase.
setConsensusCallQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field consensusCallQuality.
setConsensusMaxSeqQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field consensusMaxSeqQuality.
setConstructionProtocol(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Setter for the field constructionProtocol.
setCONTACTS(SubmissionType.CONTACTS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the contacts property.
setContig(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.ContigPosition
Setter for the field contig.
setContig(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
Setter for the field contig.
setContig(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field contig.
setContig(String) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
Setter for the field contig.
setCount(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage
Setter for the field count.
setCountFile(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field countFile.
setCoverage(HashMap<Integer, Integer>) - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage
Setter for the field coverage.
setCreateConsequenceAnnotationDB(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field createConsequenceAnnotationDB.
setCreateCoverageDB(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field createCoverageDB.
setCreated(Date) - Method in class net.sourceforge.seqware.common.model.SampleSearch
Setter for the field created.
setCreateDbSNPAnnotationDB(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field createDbSNPAnnotationDB.
setCreateMismatchDB(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field createMismatchDB.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Invoice
Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.IUS
Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Project
Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Registration
Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareStudy
Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field createTimestamp.
setCreateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Setter for the field createTimeStamp.
setCreateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Setter for the field createTimeStamp.
setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
Setter for the field createTstmp.
setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareFile
Setter for the field createTstmp.
setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareLane
Setter for the field createTstmp.
setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
Setter for the field createTstmp.
setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareSample
Setter for the field createTstmp.
setCriteria(String) - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
Setter for the field criteria.
setCurrentSelectedFiles(HttpServletRequest, List<File>) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
setCurrentSelectedFiles.
setCurrentSelectedNodes(HttpServletRequest, List<String>) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil
setCurrentSelectedNodes.
setCurrentWorkingDir(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field currentWorkingDir.
setCwd(String) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field cwd.
setCycleCoord(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Setter for the field cycleCoord.
setCYCLECOORD(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Sets the value of the cyclecoord property.
setCycleCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field cycleCount.
setCycleCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field cycleCount.
setCYCLECOUNT(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
Sets the value of the cyclecount property.
setCYCLECOUNT(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
Sets the value of the cyclecount property.
setCycleDescriptor(String) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field cycleDescriptor.
setCycleDescriptor(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field cycleDescriptor.
setCycleDescriptor(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field cycleDescriptor.
setCycles(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field cycles.
setCycles(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field cycles.
setCycleSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field cycleSequence.
setCycleSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field cycleSequence.
setCYCLESEQUENCE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
Sets the value of the cyclesequence property.
setData(ArrayList) - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
Setter for the field data.
setDatabase(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field database.
setDataDecryptionKeyString(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Sets data decryption key.
setDataEncryptionKeyString(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Sets data encryption key.
setDate(long) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
setDate(long) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
setDate(Date) - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
setDate(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
set the pre-defined date variable
setDax(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field dax.
setDaxDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setDaysUntilDue(Integer) - Method in class net.sourceforge.seqware.common.model.Invoice
Setter for the field daysUntilDue.
setDb(Connection) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
Setter for the field db.
setDb(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink
Setter for the field db.
setDb(String) - Method in class net.sourceforge.seqware.common.model.IUSLink
Setter for the field db.
setDb(String) - Method in class net.sourceforge.seqware.common.model.LaneLink
Setter for the field db.
setDb(String) - Method in class net.sourceforge.seqware.common.model.SampleLink
Setter for the field db.
setDb(String) - Method in class net.sourceforge.seqware.common.model.StudyLink
Setter for the field db.
setDB(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
Sets the value of the db property.
setDB(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
Sets the value of the db property.
setDB(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
Sets the value of the db property.
setDB(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK
Sets the value of the db property.
setDB(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
Sets the value of the db property.
setDB(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
Sets the value of the db property.
setDbmd(DatabaseMetaData) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
Setter for the field dbmd.
setDebug(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareBase
Setter for the field debug.
setDecodeMethod(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
Setter for the field decodeMethod.
setDefaultValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Setter for the field defaultValue.
setDENOVOASSEMBLY(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Sets the value of the denovoassembly property.
setDescription(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setDescription(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setDescription(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
setDescription(String) - Method in class com.github.seqware.queryengine.model.FeatureSet.Builder
 
setDescription(String) - Method in class com.github.seqware.queryengine.model.Group.Builder
 
setDescription(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet.Builder
 
setDescription(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup.Builder
 
setDescription(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryPlugin.Builder
 
setDescription(String) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.Builder
 
setDescription(String) - Method in class com.github.seqware.queryengine.model.Plugin.Builder
 
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Expense
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.File
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.IUS
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.LibrarySelection
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.LibrarySource
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Platform
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Project
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.StudyType
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
setDescription(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Setter for the field description.
setDESCRIPTION(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the description property.
setDESCRIPTION(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Sets the value of the description property.
setDescription(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Setter for the field description.
setDESCRIPTOR(StudyType.DESCRIPTOR) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Sets the value of the descriptor property.
setDESIGN(ExperimentType.DESIGN) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the design property.
setDESIGNDESCRIPTION(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
Sets the value of the designdescription property.
setDibase(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
Sets the value of the dibase property.
setDisplay(Boolean) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Setter for the field display.
setDisplay(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
setDisplayName(String) - Method in class net.sourceforge.seqware.common.model.FileType
Setter for the field displayName.
setDisplayName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Setter for the field displayName.
setDisplayName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
Setter for the field displayName.
setDisplayName(String) - Method in class net.sourceforge.solexatools.util.SummaryLine
Setter for the field displayName.
setDisplayValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Setter for the field displayValue.
setDomainObject(Registration) - Method in class net.sourceforge.seqware.common.model.RegistrationDTO
Setter for the field domainObject.
setDomainObject(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
Setter for the field domainObject.
setEarliestDate(Date) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
Set the value of earliestDate.
setEmail(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
Setter for the field email.
setEmailAddress(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setEmailAddress(String) - Method in class com.github.seqware.queryengine.model.User.Builder
 
setEmailAddress(String) - Method in class net.sourceforge.seqware.common.model.Registration
Setter for the field emailAddress.
setEnd(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
Setter for the field end.
setEndDate(Date) - Method in class net.sourceforge.seqware.common.model.Invoice
Setter for the field endDate.
setEndPage(String) - Method in class net.sourceforge.solexatools.util.PageInfo
Setter for the field endPage.
setEntityUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
Setter for the field entityUrl.
setENTREZLINK(AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
Sets the value of the entrezlink property.
setENTREZLINK(ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
Sets the value of the entrezlink property.
setENTREZLINK(RunType.RUNLINKS.RUNLINK.ENTREZLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK
Sets the value of the entrezlink property.
setENTREZLINK(SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK
Sets the value of the entrezlink property.
setENTREZLINK(StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK
Sets the value of the entrezlink property.
setErrorCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field errorCount.
setExecutionEnv(Environment.ExecutionEnvironment) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
set the execution environment
setExistingStudyType(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE
Sets the value of the existingStudyType property.
setExistingType(StudyType) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field existingType.
setExistingTypeInt(Integer) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field existingTypeInt.
setExitCode(int) - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException
Setter for the field exitCode.
setExitStatus(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field exitStatus.
setExitStatus(int) - Method in class net.sourceforge.seqware.common.module.ReturnValue
Setter for the field exitStatus.
setExpectedBaseCall(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Setter for the field expectedBaseCall.
setEXPECTEDBASECALL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Sets the value of the expectedbasecall property.
setExpectedNumberReads(Long) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field expectedNumberReads.
setExpectedNumberReads(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the expectedNumberReads property.
setExpectedNumberRuns(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field expectedNumberRuns.
setExpectedNumberRuns(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the expectedNumberRuns property.
setExpectedNumberSpots(Long) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field expectedNumberSpots.
setExpectedNumberSpots(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the expectedNumberSpots property.
setExpectedNumReads(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field expectedNumReads.
setExpectedNumRuns(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field expectedNumRuns.
setExpectedNumSpots(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field expectedNumSpots.
setExpenseId(Integer) - Method in class net.sourceforge.seqware.common.model.Expense
Setter for the field expenseId.
setExpenses(Set<Expense>) - Method in class net.sourceforge.seqware.common.model.Invoice
Setter for the field expenses.
setExpenseType(String) - Method in class net.sourceforge.seqware.common.model.Expense
Setter for the field expenseType.
setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
Setter for the field experiment.
setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ExperimentLink
Setter for the field experiment.
setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.FileReportRow
Setter for the field experiment.
setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
Setter for the field experiment.
setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field experiment.
setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
Setter for the field experiment.
setExperiment(Experiment, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setExperiment.
setExperimentAttributeId(int) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
Setter for the field experimentAttributeId.
setExperimentAttributes(Set<ExperimentAttribute>) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field experimentAttributes.
setEXPERIMENTATTRIBUTES(ExperimentType.EXPERIMENTATTRIBUTES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the experimentattributes property.
setExperimentDAO(ExperimentDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
setExperimentDAO.
setExperimentDAO(ExperimentDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
setExperimentDAO.
setExperimentDAO(ExperimentDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
Setter for the field experimentDAO.
setExperimentId(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field experimentId.
setExperimentLibraryDesign(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field experimentLibraryDesign.
setExperimentLibraryDesignDAO(ExperimentLibraryDesignDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
setExperimentLibraryDesignDAO.
setExperimentLibraryDesignDAO(ExperimentLibraryDesignDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl
setExperimentLibraryDesignDAO.
setExperimentLibraryDesignId(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Setter for the field experimentLibraryDesignId.
setExperimentLibraryDesignService(ExperimentLibraryDesignService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Setter for the field experimentLibraryDesignService.
setExperimentLinkId(int) - Method in class net.sourceforge.seqware.common.model.ExperimentLink
Setter for the field experimentLinkId.
setExperimentLinks(Set<ExperimentLink>) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field experimentLinks.
setEXPERIMENTLINKS(ExperimentType.EXPERIMENTLINKS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the experimentlinks property.
setEXPERIMENTREF(AnalysisType.PARENT.EXPERIMENTREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Sets the value of the experimentref property.
setEXPERIMENTREF(RunType.EXPERIMENTREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the experimentref property.
setExperiments(Set<Experiment>) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field experiments.
setExperiments(SortedSet<Experiment>) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field experiments.
setExperimentService(ExperimentService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
Setter for the field experimentService.
setExperimentSpotDesign(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field experimentSpotDesign.
setExperimentSpotDesign(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Setter for the field experimentSpotDesign.
setExperimentSpotDesignDAO(ExperimentSpotDesignDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService
setExperimentSpotDesignDAO.
setExperimentSpotDesignDAO(ExperimentSpotDesignDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl
setExperimentSpotDesignDAO.
setExperimentSpotDesignId(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
Setter for the field experimentSpotDesignId.
setExperimentSpotDesignReadSpecDAO(ExperimentSpotDesignReadSpecDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
setExperimentSpotDesignReadSpecDAO.
setExperimentSpotDesignReadSpecDAO(ExperimentSpotDesignReadSpecDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl
setExperimentSpotDesignReadSpecDAO.
setExperimentSpotDesignReadSpecId(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Setter for the field experimentSpotDesignReadSpecId.
setExperimentSpotDesignReadSpecService(ExperimentSpotDesignReadSpecService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Setter for the field experimentSpotDesignReadSpecService.
setExperimentSpotDesignService(ExperimentSpotDesignService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Setter for the field experimentSpotDesignService.
setExperimentSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setExpiryTime(long) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
 
setExpLibDesignDesc(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field expLibDesignDesc.
setExpLibDesignName(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field expLibDesignName.
setExpLibDesignProtocol(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field expLibDesignProtocol.
setExpLibDesignSelection(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field expLibDesignSelection.
setExpLibDesignSource(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field expLibDesignSource.
setExpLibDesignStrategy(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field expLibDesignStrategy.
setExpSpotDesignAdapterSpec(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field expSpotDesignAdapterSpec.
setExpSpotDesignReadsPerSpot(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field expSpotDesignReadsPerSpot.
setExpSpotDesignTagSpec(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field expSpotDesignTagSpec.
setExtension(String) - Method in class net.sourceforge.seqware.common.model.FileType
Setter for the field extension.
setExternalId(String) - Method in class net.sourceforge.seqware.common.model.Invoice
Setter for the field externalId.
setExternalSerializationVersion(int) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Setter for the field externalSerializationVersion.
setFactoryBackendType(SWQEFactory.Model_Type, SWQEFactory.Storage_Type, SWQEFactory.Serialization_Type) - Static method in class com.github.seqware.queryengine.factory.SWQEFactory
Used only by testing to override the back-end type
setFailed(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Setter for the field failed.
setFastqConvNum(int) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Setter for the field fastqConvNum.
setFastqConvNum(int) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Setter for the field fastqConvNum.
setFeature(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Setter for the field feature.
setFeatureACL(ACL, Feature) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
setFeatureACL.
setFeatures(int, QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
setFeatures(int, QueryEngine.FeaturePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
 
setFeatures(int, QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setFeatures(int, QESupporting.FSGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setFeatureSet(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
setFeatureSet(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
setFeatureSetACL(ACL, Reference) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
setFeatureSetACL.
setFeatureSetID(SGID) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Setter for the field featureSetID.
setFeatureSetIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
setFeatureSetIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
setFile(MultipartFile) - Method in class net.sourceforge.seqware.common.business.UploadFile
Setter for the field file.
setFile(File) - Method in class net.sourceforge.seqware.common.model.FileAttribute
Setter for the field file.
setFile(File) - Method in class net.sourceforge.seqware.common.model.FileReportRow
Setter for the field file.
setFile(File) - Method in class net.sourceforge.seqware.common.model.ShareFile
Setter for the field file.
setFile(File) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
Setter for the field file.
setFileAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.FileAttribute
Setter for the field fileAttributeId.
setFileAttributes(Set<FileAttribute>) - Method in class net.sourceforge.seqware.common.model.File
Setter for the field fileAttributes.
setFileDAO(FileDAO) - Method in interface net.sourceforge.seqware.common.business.FileService
setFileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
setFileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
Setter for the field fileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
Sets a private member variable with an instance of an implementation of FileDAO.
setFileForSequrncerRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setFileForSequrncerRun.
setFileForStudy(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setFileForStudy.
setFileForWorkflowRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setFileForWorkflowRun.
setFileForWorkflowRunRunning(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setFileForWorkflowRunRunning.
setFileId(Integer) - Method in class net.sourceforge.seqware.common.model.File
Setter for the field fileId.
setFileMetaType(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Setter for the field fileMetaType.
setFileMetaType(String) - Method in class net.sourceforge.solexatools.util.SummaryLine
Setter for the field fileMetaType.
setFilename(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setFilename(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
setFilename(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE
Sets the value of the filename property.
setFilename(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE
Sets the value of the filename property.
setFilename(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
Sets the value of the filename property.
setFileOne(MultipartFile) - Method in class net.sourceforge.seqware.common.model.UploadSequence
Setter for the field fileOne.
setFilePath(String) - Method in class net.sourceforge.seqware.common.model.File
Setter for the field filePath.
setFilePath(String) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field filePath.
setFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field filePath.
setFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field filePath.
setFilePath(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
setFilePath(File) - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
setFilePath(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field filePath.
setFilePath(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
Setter for the field filePath.
setFileReportDAO(FileReportDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
Setter for the field fileReportDAO.
setFileReportService(FileReportService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Setter for the field fileReportService.
setFileReportService(FileReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
Setter for the field fileReportService.
setFileReportService(FileReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Setter for the field fileReportService.
setFiles(Set<File>) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field files.
setFiles(List<File>) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Setter for the field files.
setFiles(ArrayList<FileMetadata>) - Method in class net.sourceforge.seqware.common.module.ReturnValue
Setter for the field files.
setFILES(RunType.DATABLOCK.FILES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Sets the value of the files property.
setFILES(SubmissionType.FILES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the files property.
setFiles(List<File>) - Method in class net.sourceforge.solexatools.util.SummaryLine
Setter for the field files.
setFiles_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Setter for the field files_url.
setFilesArray(ArrayList<File>) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
Setter for the field filesArray.
setFileService(FileService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController
Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloaderController
Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.FileController
Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.FileSetupController
Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController
Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
Setter for the field fileService.
setFileStatus(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
setFileSwa(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setFileTwo(MultipartFile) - Method in class net.sourceforge.seqware.common.model.UploadSequence
Setter for the field fileTwo.
setFileTwoURL(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
Setter for the field fileTwoURL.
setFileType(FileType) - Method in class net.sourceforge.seqware.common.business.UploadFile
Setter for the field fileType.
setFileType(FileType) - Method in class net.sourceforge.seqware.common.model.File
Setter for the field fileType.
setFileType(FileType) - Method in class net.sourceforge.seqware.common.model.UploadSequence
Setter for the field fileType.
setFiletype(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE
Sets the value of the filetype property.
setFiletype(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE
Sets the value of the filetype property.
setFileTypeDAO(FileTypeDAO) - Method in interface net.sourceforge.seqware.common.business.FileTypeService
setFileTypeDAO.
setFileTypeDAO(FileTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl
setFileTypeDAO.
setFileTypeDAO(FileTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
Setter for the field fileTypeDAO.
setFileTypeId(Integer) - Method in class net.sourceforge.seqware.common.business.UploadFile
Setter for the field fileTypeId.
setFileTypeId(Integer) - Method in class net.sourceforge.seqware.common.model.FileType
Setter for the field fileTypeId.
setFileTypeId(Integer) - Method in class net.sourceforge.seqware.common.model.UploadSequence
Setter for the field fileTypeId.
setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
Setter for the field fileTypeService.
setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
Setter for the field fileTypeService.
setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Setter for the field fileTypeService.
setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
Setter for the field fileTypeService.
setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
Setter for the field fileTypeService.
setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
Setter for the field fileTypeService.
setFileUploadService(FileUploadService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Setter for the field fileUploadService.
setFileURL(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
Setter for the field fileURL.
setFileURL(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
Setter for the field fileURL.
setFinalized(boolean) - Method in class net.sourceforge.seqware.common.model.Invoice
Setter for the field finalized.
setFinishedTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Expense
Setter for the field finishedTimestamp.
setFirstName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setFirstName(String) - Method in class com.github.seqware.queryengine.model.User.Builder
 
setFirstName(String) - Method in class net.sourceforge.seqware.common.model.Registration
Setter for the field firstName.
setFirstName(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
Setter for the field firstName.
setFlowCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field flowCount.
setFlowCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field flowCount.
setFLOWCOUNT(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
Sets the value of the flowcount property.
setFLOWCOUNT(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
Sets the value of the flowcount property.
setFlowSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field flowSequence.
setFlowSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field flowSequence.
setFLOWSEQUENCE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
Sets the value of the flowsequence property.
setFLOWSEQUENCE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
Sets the value of the flowsequence property.
setFolderStore(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
Setter for the field folderStore.
setFolderStore(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
Setter for the field folderStore.
setForceCopy(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
when forceCopy is true, it will pass "--forcecopy" argument to provisionFileJob
setForceRunAll(Boolean) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
setFormatCode(Integer) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Sets the value of the formatCode property.
setFrame(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Setter for the field frame.
setFriendlyRowkey(String) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.FeatureSet.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.Group.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.impl.FeatureList.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.interfaces.BaseBuilder
Set a friendly rowKey for the atom to be built.
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.Plugin.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.PluginRun.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.Reference.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.ReferenceSet.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.Tag.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.TagSet.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.User.Builder
 
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.util.FSGID
Setter for the field friendlyRowKey.
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.util.SGID
Setter for the field friendlyRowKey.
setFs_default_name(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setFs_defaultFS(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setFs_hdfs_impl(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setFullyPaid(boolean) - Method in class net.sourceforge.seqware.common.model.Invoice
Setter for the field fullyPaid.
setFuzzyStartPositionMax(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field fuzzyStartPositionMax.
setFuzzyStopPositionMin(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field fuzzyStopPositionMin.
setGcrOutputFile(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
 
setGcrSkipIfMissing(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
 
setGcrSkipIfOutputExists(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
 
setGeneChr(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Setter for the field geneChr.
setGeneId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Setter for the field geneId.
setGeneId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Setter for the field geneId.
setGenomeId(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field genomeId.
setGenomicSequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Setter for the field genomicSequence.
setGroup(Group) - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder
Set the group permissions
setGroup(SGID) - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder
Set the SGID for the group permissions
setGroup(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Setter for the field group.
setGroupACL(ACL, Group) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
setGroupACL.
setGroupingStrategy(FindAllTheFiles.Header) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
setGrp(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
setGrp(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
setGrps(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setGrps(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setHandle(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the handle property.
setHasMetadataWriteback(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
setHasMetadataWriteback(boolean) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
job specific metadata is not supported yet
setHbase_master(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setHbase_zookeeper_property_clientPort(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setHbase_zookeeper_quorum(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setHeader(FindAllTheFiles.Header) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
Deprecated. 
setHeader(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.RunInfo
 
setHELICOS(ExperimentType.PLATFORM.HELICOS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
Sets the value of the helicos property.
setHOLD(SubmissionType.ACTIONS.ACTION.HOLD) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Sets the value of the hold property.
setHoldForPeriod(Integer) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
Sets the value of the holdForPeriod property.
setHoldUntilDate(XMLGregorianCalendar) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
Sets the value of the holdUntilDate property.
setHost(String) - Method in class net.sourceforge.seqware.common.model.Workflow
Deprecated.  
setHost(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field host.
setHost(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Setter for the field host.
setHtml(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field html.
setHtml(String) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field html.
setHtml(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field html.
setHYBRIDASSEMBLY(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Sets the value of the hybridassembly property.
setId(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setId(Integer) - Method in class net.sourceforge.seqware.common.business.UploadFile
Setter for the field id.
setId(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink
Setter for the field id.
setId(String) - Method in class net.sourceforge.seqware.common.model.IUSLink
Setter for the field id.
setId(String) - Method in class net.sourceforge.seqware.common.model.LaneLink
Setter for the field id.
setId(String) - Method in class net.sourceforge.seqware.common.model.SampleLink
Setter for the field id.
setId(String) - Method in class net.sourceforge.seqware.common.model.StudyLink
Setter for the field id.
setId(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
set the job id
setId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
setId.
setId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Model
setId.
setId(String) - Method in interface net.sourceforge.seqware.queryengine.backend.model.ModelInterface
setId.
setId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.StringId
Setter for the field id.
setID(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
Sets the value of the id property.
setID(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
Sets the value of the id property.
setID(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
Sets the value of the id property.
setID(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK
Sets the value of the id property.
setID(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
Sets the value of the id property.
setID(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
Sets the value of the id property.
setIdentitySamples(Collection<Sample>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
Setter for the field identitySamples.
setILLUMINA(ExperimentType.PLATFORM.ILLUMINA) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
Sets the value of the illumina property.
setIncludeCoverage(boolean) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Setter for the field includeCoverage.
setIncludeCoverage(boolean) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Setter for the field includeCoverage.
setIncludeIndels(boolean) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Setter for the field includeIndels.
setIncludeIndels(boolean) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Setter for the field includeIndels.
setIncludeIndels(boolean) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Setter for the field includeIndels.
setIncludeSNV(boolean) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Setter for the field includeSNV.
setIncludeSNV(boolean) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Setter for the field includeSNV.
setIncludeSNVs(boolean) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Setter for the field includeSNVs.
setIndividualName(String) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field individualName.
setInfo(String) - Method in class net.sourceforge.solexatools.util.PageInfo
Setter for the field info.
setInformOnError(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
Sets the value of the informOnError property.
setInformOnStatus(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
Sets the value of the informOnStatus property.
setIniFile(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field iniFile.
setInput(String) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Setter for the field input.
setInput(String) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Setter for the field input.
setInputAlgorithm(String) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field inputAlgorithm.
setInputFiles(Collection<File>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
Setter for the field inputFiles.
setInstalled(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
 
setInstitution(String) - Method in class net.sourceforge.seqware.common.model.Registration
Setter for the field institution.
setInstitution(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
Setter for the field institution.
setInstrumentModel(String) - Method in class net.sourceforge.seqware.common.model.Platform
Setter for the field instrumentModel.
setINSTRUMENTMODEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
Sets the value of the instrumentmodel property.
setINSTRUMENTMODEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
Sets the value of the instrumentmodel property.
setINSTRUMENTMODEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
Sets the value of the instrumentmodel property.
setINSTRUMENTMODEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
Sets the value of the instrumentmodel property.
setInstrumentModel(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the instrumentModel property.
setInstrumentName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field instrumentName.
setInstrumentName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field instrumentName.
setInstrumentName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the instrumentName property.
setInvitationCode(String) - Method in class net.sourceforge.seqware.common.model.Registration
Setter for the field invitationCode.
setInvoice(Invoice) - Method in class net.sourceforge.seqware.common.model.Expense
Setter for the field invoice.
setInvoiceDAO(InvoiceDAO) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
setInvoiceDAO.
setInvoiceDAO(InvoiceDAO) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
setInvoiceDAO.
setInvoiceId(Integer) - Method in class net.sourceforge.seqware.common.model.Invoice
Setter for the field invoiceId.
setInvoiceService(InvoiceService) - Method in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController
Setter for the field invoiceService.
setInvoiceService(InvoiceService) - Method in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController
Setter for the field invoiceService.
setIsEnd(boolean) - Method in class net.sourceforge.solexatools.util.PageInfo
Setter for the field isEnd.
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field isHasFile.
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.IUS
Setter for the field isHasFile.
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field isHasFile.
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field isHasFile.
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field isHasFile.
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field isHasFile.
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field isHasFile.
setIsInput(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
isInput = @param isInput isOutput = !@param isInput
setIsOutput(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
isInput = !@param isOutput isOutput = @param isOutput
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field isSelected.
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.File
Setter for the field isSelected.
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.IUS
Setter for the field isSelected.
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field isSelected.
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field isSelected.
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field isSelected.
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field isSelected.
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field isSelected.
setIsStart(boolean) - Method in class net.sourceforge.solexatools.util.PageInfo
Setter for the field isStart.
setItemRgb(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Setter for the field itemRgb.
setIus(IUS) - Method in class net.sourceforge.seqware.common.model.FileReportRow
Setter for the field ius.
setIus(IUS) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
Setter for the field ius.
setIus(IUS) - Method in class net.sourceforge.seqware.common.model.IUSLink
Setter for the field ius.
setIUS(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.Lane
setIUS.
setIUS(Set<IUS>) - Method in class net.sourceforge.seqware.common.model.Processing
setIUS.
setIus(IUS) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
Setter for the field ius.
setIUS(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.Sample
setIUS.
setIus(IUS) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
Setter for the field ius.
setIus(IUS) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
Setter for the field ius.
setIus(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field ius.
setIus(IUS) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
Setter for the field ius.
setIusAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
Setter for the field iusAttributeId.
setIusAttributes(Set<IUSAttribute>) - Method in class net.sourceforge.seqware.common.model.IUS
Setter for the field iusAttributes.
setIUSDAO(IUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
setIUSDAO.
setIUSDAO(IUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
setIUSDAO.
setIUSDAO(IUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
Sets a private member variable with an instance of an implementation of IUSDAO.
setIUSDAO(IUSDAO) - Method in interface net.sourceforge.seqware.common.business.IUSService
setIUSDAO.
setIusId(Integer) - Method in class net.sourceforge.seqware.common.model.IUS
Setter for the field iusId.
setIusLinkId(int) - Method in class net.sourceforge.seqware.common.model.IUSLink
Setter for the field iusLinkId.
setIusLinks(Set<IUSLink>) - Method in class net.sourceforge.seqware.common.model.IUS
Setter for the field iusLinks.
setIusService(IUSService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field iusService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
Setter for the field iusService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
setIUSService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
setIUSService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
Setter for the field iusService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController
setIUSService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.IUSSetupController
Setter for the field iusService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
Setter for the field iusService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
setIUSService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
Setter for the field iusService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
setIUSService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
setIUSService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
Setter for the field iusService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
setIUSService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
Setter for the field iusService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
setIUSService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
Setter for the field iusService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
setIUSService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
setIUSService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Setter for the field iusService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
setIUSService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
Setter for the field iusService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
setIUSService.
setIusSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setJdbcTemplate(SimpleJdbcTemplate) - Method in class net.sourceforge.seqware.pipeline.runner.LogAspect
Setter for the field jdbcTemplate.
setJoinDevelopersMailingList(boolean) - Method in class net.sourceforge.seqware.common.model.Registration
Setter for the field joinDevelopersMailingList.
setJoinUsersMailingList(boolean) - Method in class net.sourceforge.seqware.common.model.Registration
Setter for the field joinUsersMailingList.
setKey(String) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setKey(String) - Method in class com.github.seqware.queryengine.model.Tag.Builder
' Should not be called outside of the back-end
setKey(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Setter for the field key.
setKey(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
Setter for the field key.
setKey(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
Setter for the field key.
setKey(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
Setter for the field key.
setKeyIndex(String) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Setter for the field keyIndex.
setKeyvalues(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Model
Setter for the field keyvalues.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink
Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.IUSLink
Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.LaneLink
Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.SampleLink
Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.StudyLink
Setter for the field label.
setLABEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
Sets the value of the label property.
setLABEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
Sets the value of the label property.
setLABEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK
Sets the value of the label property.
setLABEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
Sets the value of the label property.
setLABEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK
Sets the value of the label property.
setLabName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the labName property.
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.FileReportRow
Setter for the field lane.
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.IUS
Setter for the field lane.
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
Setter for the field lane.
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.LaneLink
Setter for the field lane.
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
Setter for the field lane.
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
Setter for the field lane.
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
Setter for the field lane.
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.ShareLane
Setter for the field lane.
setLane(String) - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Set the value of lane
setLane(Integer) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
setLane1(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field lane1.
setLane2(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field lane2.
setLane3(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field lane3.
setLane4(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field lane4.
setLane5(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field lane5.
setLane6(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field lane6.
setLane7(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field lane7.
setLane8(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field lane8.
setLane_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Setter for the field lane_url.
setLaneAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
Setter for the field laneAttributeId.
setLaneAttributes(Set<LaneAttribute>) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field laneAttributes.
setLaneCount(int) - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
Setter for the field laneCount.
setLaneDAO(LaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
Setter for the field laneDAO.
setLaneDAO(LaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
setLaneDAO.
setLaneDAO(LaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
Sets a private member variable with an instance of an implementation of LaneDAO.
setLaneDAO(LaneDAO) - Method in interface net.sourceforge.seqware.common.business.LaneService
setLaneDAO.
setLaneForSequrncerRun(Lane, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setLaneForSequrncerRun.
setLaneForStudy(Lane, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setLaneForStudy.
setLaneId(Integer) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field laneId.
setLaneIndex(Integer) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field laneIndex.
setLaneLinkId(int) - Method in class net.sourceforge.seqware.common.model.LaneLink
Setter for the field laneLinkId.
setLaneLinks(Set<LaneLink>) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field laneLinks.
setLanes(Set<Lane>) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field lanes.
setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field lanes.
setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field lanes.
setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field lanes.
setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field lanes.
setLaneService(LaneService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.validation.LaneValidator
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSetupController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
Setter for the field laneService.
setLanesForView(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.Sample
setLanesForView.
setLaneString(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
setLaneSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setLastName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setLastName(String) - Method in class com.github.seqware.queryengine.model.User.Builder
 
setLastName(String) - Method in class net.sourceforge.seqware.common.model.Registration
Setter for the field lastName.
setLastName(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto
Setter for the field lastName.
setLatestDate(Date) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
Set the value of latestDate.
setLayout(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Setter for the field layout.
setLeastSigBits(long) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
setLength(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Setter for the field length.
setLIBRARYCONSTRUCTIONPROTOCOL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Sets the value of the libraryconstructionprotocol property.
setLIBRARYDESCRIPTOR(ExperimentType.DESIGN.LIBRARYDESCRIPTOR) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
Sets the value of the librarydescriptor property.
setLibraryId(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto
Setter for the field libraryId.
setLIBRARYLAYOUT(ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Sets the value of the librarylayout property.
setLIBRARYNAME(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Sets the value of the libraryname property.
setLibrarySamples(Collection<Sample>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
Setter for the field librarySamples.
setLibrarySelection(LibrarySelection) - Method in class net.sourceforge.seqware.common.model.Lane
 
setLIBRARYSELECTION(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Sets the value of the libraryselection property.
setLibrarySelectionDAO(LibrarySelectionDAO) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl
setLibrarySelectionDAO.
setLibrarySelectionDAO(LibrarySelectionDAO) - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService
setLibrarySelectionDAO.
setLibrarySelectionId(Integer) - Method in class net.sourceforge.seqware.common.model.LibrarySelection
Setter for the field librarySelectionId.
setLibrarySelectionService(LibrarySelectionService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setLibrarySelectionService(LibrarySelectionService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Setter for the field librarySelectionService.
setLibrarySelectionService(LibrarySelectionService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
Setter for the field librarySelectionService.
setLibraryService(LibraryService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field libraryService.
setLibrarySource(LibrarySource) - Method in class net.sourceforge.seqware.common.model.Lane
 
setLIBRARYSOURCE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Sets the value of the librarysource property.
setLibrarySourceDAO(LibrarySourceDAO) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl
setLibrarySourceDAO.
setLibrarySourceDAO(LibrarySourceDAO) - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService
setLibrarySourceDAO.
setLibrarySourceId(Integer) - Method in class net.sourceforge.seqware.common.model.LibrarySource
Setter for the field librarySourceId.
setLibrarySourceService(LibrarySourceService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setLibrarySourceService(LibrarySourceService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Setter for the field librarySourceService.
setLibrarySourceService(LibrarySourceService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
Setter for the field librarySourceService.
setLibraryStrategy(LibraryStrategy) - Method in class net.sourceforge.seqware.common.model.Lane
 
setLIBRARYSTRATEGY(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
Sets the value of the librarystrategy property.
setLibraryStrategyDAO(LibraryStrategyDAO) - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl
setLibraryStrategyDAO.
setLibraryStrategyDAO(LibraryStrategyDAO) - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService
setLibraryStrategyDAO.
setLibraryStrategyId(Integer) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
Setter for the field libraryStrategyId.
setLibraryStrategyService(LibraryStrategyService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setLibraryStrategyService(LibraryStrategyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Setter for the field libraryStrategyService.
setLibraryStrategyService(LibraryStrategyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
Setter for the field libraryStrategyService.
setLibraryType(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
Setter for the field libraryType.
setLIMSAdmin(boolean) - Method in class net.sourceforge.seqware.common.model.Registration
setLIMSAdmin.
setList(List<Experiment>) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentList
setList.
setList(List<File>) - Method in class net.sourceforge.seqware.common.model.lists.FileList
setList.
setList(List<IUS>) - Method in class net.sourceforge.seqware.common.model.lists.IUSList
setList.
setList(List<Lane>) - Method in class net.sourceforge.seqware.common.model.lists.LaneList
setList.
setList(List<LibrarySelection>) - Method in class net.sourceforge.seqware.common.model.lists.LibrarySelectionList
setList.
setList(List<LibrarySource>) - Method in class net.sourceforge.seqware.common.model.lists.LibrarySourceList
setList.
setList(List<LibraryStrategy>) - Method in class net.sourceforge.seqware.common.model.lists.LibraryStrategyList
setList.
setList(List<Organism>) - Method in class net.sourceforge.seqware.common.model.lists.OrganismList
setList.
setList(List<Platform>) - Method in class net.sourceforge.seqware.common.model.lists.PlatformList
setList.
setList(List<Processing>) - Method in class net.sourceforge.seqware.common.model.lists.ProcessingList
setList.
setList(List<ReturnValue>) - Method in class net.sourceforge.seqware.common.model.lists.ReturnValueList
setList.
setList(List<Sample>) - Method in class net.sourceforge.seqware.common.model.lists.SampleList
setList.
setList(List<SequencerRun>) - Method in class net.sourceforge.seqware.common.model.lists.SequencerRunList
setList.
setList(List<Study>) - Method in class net.sourceforge.seqware.common.model.lists.StudyList
setList.
setList(List<StudyType>) - Method in class net.sourceforge.seqware.common.model.lists.StudyTypeList
setList.
setList(List<Workflow>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowList
setList.
setList(List<WorkflowParam>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamList
setList.
setList(List<WorkflowParamValue>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList
setList.
setList(Collection<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList
setList.
setList(List<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2
setList.
setLocal() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
setLocal(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
setLocal() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
Sets this job to run locally.
setLocal(boolean) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
Sets whether this job should run locally.
setLS454(ExperimentType.PLATFORM.LS454) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
Sets the value of the ls454 property.
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.FeatureSet.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.Group.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Set the model manager for this Atom
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.impl.FeatureList.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.interfaces.BaseBuilder
Set a manager for this Atom
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.Plugin.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.PluginRun.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.Reference.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.ReferenceSet.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.Tag.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.TagSet.Builder
 
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.User.Builder
 
setMapred_job_tracker(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setMaxCoverage(int) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Setter for the field maxCoverage.
setMaxCoverage(int) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Setter for the field maxCoverage.
setMaxCoverage(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Setter for the field maxCoverage.
setMaximumMappingQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field maximumMappingQuality.
setMaximumMappingQuality(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field maximumMappingQuality.
setMaxLockers(int) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field maxLockers.
setMaxLockObjects(int) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field maxLockObjects.
setMaxLocks(int) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field maxLocks.
setMaxMemory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
setMaxMemory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
 
setMaxMemory(String) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
set max memory
setMd5sum(String) - Method in class net.sourceforge.seqware.common.model.File
Setter for the field md5sum.
setMd5sum(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
setMd5sum(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
setMd5sum(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
Setter for the field md5sum.
setMEMBERS(SampleType.MEMBERS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Sets the value of the members property.
setMemory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setMemReq(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Setter for the field memReq.
setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
Setter for the field metadata.
setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.decider.Decider
Lets you set the metadata object
setMetadata(Metadata) - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Lets you set the metadata object
setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.module.Module
Setter for the field metadata.
setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
Lets you set the metadata object
setMetadata(Metadata) - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Lets you set the metadata object
setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
Lets you set the metadata object
setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
Lets you set the metadata object
setMetadataOutputPrefix(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob
 
setMetadataOutputPrefix(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob
 
setMetadataWriteback(Boolean) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
setMetadataWriteBack(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
need metadata writeback? user can override this setting by using --no-metadata or --metadata from command line
setMetadataWriteback(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
setMetadataWriteback(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
setMetaType(String) - Method in class net.sourceforge.seqware.common.model.File
Setter for the field metaType.
setMetaType(String) - Method in class net.sourceforge.seqware.common.model.FileType
Setter for the field metaType.
setMetaType(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
setMetaType(List<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
setMetaType(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
Setter for the field metaType.
setMetaws(MetadataWS) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
setMimeType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
setMinCoverage(int) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Setter for the field minCoverage.
setMinCoverage(int) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Setter for the field minCoverage.
setMinCoverage(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Setter for the field minCoverage.
setMinObservations(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Setter for the field minObservations.
setMinObservationsPerStrand(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Setter for the field minObservationsPerStrand.
setMinPercent(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Setter for the field minPercent.
setMinSnpQuality(float) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Setter for the field minSnpQuality.
setMinSnpQuality(float) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Setter for the field minSnpQuality.
setMinSNVPhred(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Setter for the field minSNVPhred.
setMismatchAAChangeBlosumScore(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Setter for the field mismatchAAChangeBlosumScore.
setMismatchAminoAcidChange(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Setter for the field mismatchAminoAcidChange.
setMismatchChr(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Setter for the field mismatchChr.
setMismatchCodonChange(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Setter for the field mismatchCodonChange.
setMismatchCodonPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Setter for the field mismatchCodonPosition.
setMismatchId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Setter for the field mismatchId.
setMismatchStart(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Setter for the field mismatchStart.
setMismatchStop(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Setter for the field mismatchStop.
setMismatchType(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Setter for the field mismatchType.
setMODIFY(SubmissionType.ACTIONS.ACTION.MODIFY) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Sets the value of the modify property.
setModuleParameter(List<String>) - Method in class net.sourceforge.seqware.pipeline.runner.Runner2
Setter for the field moduleParameter.
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setMostSigBits(long) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
setMULTIPLIER(double) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
Sets the value of the multiplier property.
setMutatedGenomicSequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Setter for the field mutatedGenomicSequence.
setMutatedTranslatedSequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Setter for the field mutatedTranslatedSequence.
setName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.Group.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryPlugin.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.Plugin.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.Reference.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.ReferenceSet.Builder
 
setName(String) - Method in class com.github.seqware.queryengine.model.TagSet.Builder
 
setName(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.IUS
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.LibrarySelection
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.LibrarySource
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.Organism
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.Platform
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.Project
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.StudyType
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Set the value of name
setName(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
set the workflow name
setName(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
 
setName(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Sets the value of the name property.
setName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
Sets the value of the name property.
setName(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto
Setter for the field name.
setName(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
setNameNode(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
Setter for the field nameNode.
setNamespace(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
 
setNamespace(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
setNamespace.
setNamespace(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
 
setNcbiTaxId(Integer) - Method in class net.sourceforge.seqware.common.model.Organism
Setter for the field ncbiTaxId.
setNcbiTaxonomyId(Integer) - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto
Setter for the field ncbiTaxonomyId.
setNetwork(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setNetworkReq(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Setter for the field networkReq.
setNewStudyType(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE
Sets the value of the newStudyType property.
setNewType(String) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field newType.
SetNodeIdInSession - Class in net.sourceforge.solexatools.util
SetNodeIdInSession class.
SetNodeIdInSession() - Constructor for class net.sourceforge.solexatools.util.SetNodeIdInSession
 
setNominalLength(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Setter for the field nominalLength.
setNOMINALLENGTH(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
Sets the value of the nominallength property.
setNominalSdev(Long) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Setter for the field nominalSdev.
setNOMINALSDEV(Double) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
Sets the value of the nominalsdev property.
setNotes(String) - Method in class net.sourceforge.seqware.common.model.Invoice
Setter for the field notes.
setNotes(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
Sets the value of the notes property.
setNotes(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
Sets the value of the notes property.
setNotes(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
Sets the value of the notes property.
setNotes(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE
Sets the value of the notes property.
setNotes(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS
Sets the value of the notes property.
setNotes(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
Sets the value of the notes property.
setNotRunned(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Setter for the field notRunned.
setNumberChannels(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Sets the value of the numberChannels property.
setNUMBEROFLEVELS(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
Sets the value of the numberoflevels property.
setNUMBEROFREADSPERSPOT(long) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
Sets the value of the numberofreadsperspot property.
setOffspringProcessings(SortedSet<Processing>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field offspringProcessings.
setOkTo(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
setOOZIE_APP_PATH(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setOOZIE_APP_ROOT(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setOOZIE_JOBTRACKER(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setOOZIE_NAMENODE(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setOOZIE_QUEUENAME(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setOOZIE_URL(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setOOZIE_WORK_DIR(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setOrganism(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setOrganism(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet.Builder
 
setOrganism(String) - Method in class com.github.seqware.queryengine.model.ReferenceSet.Builder
 
setOrganism(String) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field organism.
setOrganism(Organism) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field organism.
setOrganism(String) - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Set the value of organism
setOrganism(OrganismDto) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Setter for the field organism.
setOrganismDAO(OrganismDAO) - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl
setOrganismDAO.
setOrganismDAO(OrganismDAO) - Method in interface net.sourceforge.seqware.common.business.OrganismService
setOrganismDAO.
setOrganismId(Integer) - Method in class net.sourceforge.seqware.common.model.Organism
Setter for the field organismId.
setOrganismId(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field organismId.
setOrganismService(OrganismService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setOrganismService(OrganismService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
Setter for the field organismService.
setOrganismService(OrganismService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
Setter for the field organismService.
setORIENTATION(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
Sets the value of the orientation property.
setOriginalFileName(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Setter for the field originalFileName.
setOs(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
 
setOutputDir(String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
Setter for the field outputDir.
setOutputDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieProvisionFileJob
 
setOutputDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob
 
setOutputFilename(String) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
Setter for the field outputFilename.
setOutputFilename(String) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Setter for the field outputFilename.
setOutputFiles(Collection<File>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
Setter for the field outputFiles.
setOutputPath(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
 
setOwner(SGID) - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder
Set the SGID for the owner permissions
setOwner(User) - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder
Set the user permissions
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.File
Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Invoice
Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.IUS
Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field owner.
setOwner(OwnerDto) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Setter for the field owner.
setOwnerId(Integer) - Method in class net.sourceforge.seqware.common.model.Project
Setter for the field ownerId.
setOwnerUserName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setPage(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
Setter for the field page.
setPaidAmount(Double) - Method in class net.sourceforge.seqware.common.model.Invoice
Setter for the field paidAmount.
setPAIRED(ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
Sets the value of the paired property.
setPairedEnd(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field pairedEnd.
setPairedEnd(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field pairedEnd.
setPairedFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field pairedFilePath.
setPairedFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field pairedFilePath.
setPairedOrientation(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Setter for the field pairedOrientation.
setParameter(RPNStack.Parameter, Object) - Method in class com.github.seqware.queryengine.kernel.RPNStack
Sets a parameter to a concrete value.
setParameters(ByteString) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
setParameters(List<Object>) - Method in class com.github.seqware.queryengine.model.PluginRun.Builder
Set the group for the current Atom
setParameters(String) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field parameters.
setParameters(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
Setter for the field parameters.
setParameters(List<String>) - Method in class net.sourceforge.seqware.pipeline.module.Module
setParameters.
setParameters(List<String>) - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface
setParameters.
setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.decider.Decider
Lets you set a List of params so the plugin can deal with parameters
setParams(List<String>) - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface
Lets you set a List of params so the plugin can deal with parameters
setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin
Lets you set a List of params so the plugin can deal with parameters
setParams(List<String>) - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
Lets you set a List of params so the plugin can deal with parameters
setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld
Lets you set a List of params so the plugin can deal with parameters
setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugins.MarkdownPlugin
Lets you set a List of params so the plugin can deal with parameters
setParams(SortedSet<WorkflowParam>) - Method in class net.sourceforge.solexatools.util.SummaryLine
Setter for the field params.
setPARENT(AnalysisType.PARENT) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the parent property.
setParentAccessions(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
setParentAccessions(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
setParentAccessions(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
setParentAccessions(Collection<String>) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
set parent accessiosns for the job
setParentAccessions(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
set the parent accessions for provision file job
setParentId(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy
 
setParentProcessingAccession(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
Setter for the field parentProcessingAccession.
setParentProcessings(Collection<Processing>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
Setter for the field parentProcessings.
setParents(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field parents.
setParents(Set<Sample>) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field parents.
setParents(Collection<Job>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
set parent jobs
setParentSample(String) - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Set the value of parentSample
setParentUrls(Set<String>) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Setter for the field parentUrls.
setParentWorkflowAccessions(Set<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
setPassword(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setPassword(String) - Method in class com.github.seqware.queryengine.model.User.Builder
 
setPassword(String) - Method in class net.sourceforge.seqware.common.model.Registration
Setter for the field password.
setPassword(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field password.
setPasswordHint(String) - Method in class net.sourceforge.seqware.common.model.Registration
Setter for the field passwordHint.
setPasswordWithoutHash(String) - Method in class com.github.seqware.queryengine.model.User.Builder
 
setPathToFirstFile(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
Setter for the field pathToFirstFile.
setPathToSecondFile(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
Setter for the field pathToSecondFile.
setPayee(boolean) - Method in class net.sourceforge.seqware.common.model.Registration
Setter for the field payee.
setPeakMemory(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
set the max memory for the workflow
setPeakThreads(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
set the max threads for the workflow
setPegasusConfigDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setPending(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Setter for the field pending.
setPermanentBundleLocation(String) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field permanentBundleLocation.
setPermBundleLocation(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Setter for the field permBundleLocation.
setPermissions(ACL) - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl
Set permissions for this
setPermissions(ACL) - Method in interface com.github.seqware.queryengine.model.interfaces.ACLable
Set permissions for this
setPfn(Pfn) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
 
setPhase(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setPhase(String) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setPlatform(Platform) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field platform.
setPlatform(Platform) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field platform.
setPlatform(Platform) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field platform.
setPLATFORM(ExperimentType.PLATFORM) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the platform property.
setPlatformDAO(PlatformDAO) - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl
setPlatformDAO.
setPlatformDAO(PlatformDAO) - Method in interface net.sourceforge.seqware.common.business.PlatformService
setPlatformDAO.
setPlatformId(Integer) - Method in class net.sourceforge.seqware.common.model.Platform
Setter for the field platformId.
setPlatformInt(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field platformInt.
setPlatformInt(int) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field platformInt.
setPlatformService(PlatformService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field platformService.
setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Setter for the field platformService.
setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
Setter for the field platformService.
setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Setter for the field platformService.
setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
Setter for the field platformService.
setPluginRunIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
setPluginRunIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
setPluginRunner(PluginRunnerInterface) - Method in class com.github.seqware.queryengine.model.PluginRun.Builder
 
setPmi(Importer) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Setter for the field pmi.
setPmi(Importer) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Setter for the field pmi.
setPostgresqlPersistenceStrategy(int) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field postgresqlPersistenceStrategy.
setPragma(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setPragma(String) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setPrecedingID(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
setPrecedingID(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
setPrecedingID(QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
setPrecedingID(QESupporting.FSGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
setPrecedingSGID(SGID) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Used in back-end to set previous version without side-effects
setPrecedingVersion(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setPrecedingVersion(QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setPrecedingVersion(QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setPrecedingVersion(QueryEngine.FeaturePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setPrecedingVersion(QueryEngine.FeatureSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setPrecedingVersion(QueryEngine.FeatureSetPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setPrecedingVersion(QueryEngine.GroupPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setPrecedingVersion(QueryEngine.GroupPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setPrecedingVersion(QueryEngine.PluginPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
setPrecedingVersion(QueryEngine.PluginPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB.Builder
 
setPrecedingVersion(QueryEngine.PluginRunPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
setPrecedingVersion(QueryEngine.PluginRunPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB.Builder
 
setPrecedingVersion(QueryEngine.ReferencePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
setPrecedingVersion(QueryEngine.ReferencePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
 
setPrecedingVersion(QueryEngine.ReferenceSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setPrecedingVersion(QueryEngine.ReferenceSetPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setPrecedingVersion(QueryEngine.TagSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
setPrecedingVersion(QueryEngine.TagSetPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
setPrecedingVersion(QueryEngine.UserPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setPrecedingVersion(QueryEngine.UserPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
 
setPrecedingVersion(T) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Explicitly set the previous version of a Atom.
setPrecedingVersion(T) - Method in interface com.github.seqware.queryengine.model.interfaces.Versionable
Explicitly set the previous version of a Atom.
setPredicate(String) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setPredicate(String) - Method in class com.github.seqware.queryengine.model.Tag.Builder
 
setPricePerUnit(Double) - Method in class net.sourceforge.seqware.common.model.Expense
Setter for the field pricePerUnit.
setPrivate(boolean) - Method in class net.sourceforge.seqware.common.model.Workflow
setPrivate.
setProcCountInfo(List<SequencerRun>) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
setProcCountInfo.
setProcCountInfo(List<SequencerRun>) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
setProcCountInfo.
setProcess(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field process.
setProcessedCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field processedCount.
setProcessExitStatus(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field processExitStatus.
setProcessExitStatus(int) - Method in class net.sourceforge.seqware.common.module.ReturnValue
Setter for the field processExitStatus.
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.FileReportRow
Setter for the field processing.
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
Setter for the field processing.
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
Setter for the field processing.
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
Setter for the field processing.
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
Setter for the field processing.
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
Setter for the field processing.
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
Setter for the field processing.
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
Setter for the field processing.
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
Setter for the field processing.
setPROCESSING(ExperimentType.PROCESSING) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the processing property.
setProcessingAccession(int) - Method in class net.sourceforge.seqware.pipeline.module.Module
Setter for the field processingAccession.
setProcessingAttributeId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
Setter for the field processingAttributeId.
setProcessingAttributes(Set<ProcessingAttribute>) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field processingAttributes.
setProcessingByChildId(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
Setter for the field processingByChildId.
setProcessingByParentId(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
Setter for the field processingByParentId.
setProcessingCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field processingCount.
setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
Setter for the field processingDAO.
setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
Sets a private member variable with an instance of an implementation of ProcessingDAO.
setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
setProcessingDAO.
setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
Setter for the field processingDAO.
setProcessingDAO(ProcessingDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
setProcessingDAO.
setProcessingExperimentsDAO(ProcessingExperimentsDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
setProcessingExperimentsDAO.
setProcessingExperimentsDAO(ProcessingExperimentsDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService
setProcessingExperimentsDAO.
setProcessingExperimentsId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
Setter for the field processingExperimentsId.
setProcessingExperimentsService(ProcessingExperimentsService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field processingExperimentsService.
setProcessingForSequrncerRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setProcessingForSequrncerRun.
setProcessingForStudy(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setProcessingForStudy.
setProcessingForWorkflowRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setProcessingForWorkflowRun.
setProcessingForWorkflowRunRunning(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setProcessingForWorkflowRunRunning.
setProcessingId(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field processingId.
setProcessingIUSDAO(ProcessingIUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
setProcessingIUSDAO.
setProcessingIUSDAO(ProcessingIUSDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService
setProcessingIUSDAO.
setProcessingIusId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
Setter for the field processingIusId.
setProcessingIusService(ProcessingIUSService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field processingIusService.
setProcessingLanesDAO(ProcessingLanesDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
setProcessingLanesDAO.
setProcessingLanesDAO(ProcessingLanesDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService
setProcessingLanesDAO.
setProcessingLaneService(ProcessingLanesService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field processingLaneService.
setProcessingLanesId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
Setter for the field processingLanesId.
setProcessingRelationshipDAO(ProcessingRelationshipDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
setProcessingRelationshipDAO.
setProcessingRelationshipDAO(ProcessingRelationshipDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService
setProcessingRelationshipDAO.
setProcessingRelationshipId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
Setter for the field processingRelationshipId.
setProcessingRelationshipService(ProcessingRelationshipService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field processingRelationshipService.
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field processings.
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.File
Setter for the field processings.
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.IUS
Setter for the field processings.
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field processings.
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field processings.
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field processings.
setProcessings(SortedSet<Processing>) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field processings.
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field processings.
setProcessings(SortedSet<Processing>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field processings.
setProcessingSamplesDAO(ProcessingSamplesDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
setProcessingSamplesDAO.
setProcessingSamplesDAO(ProcessingSamplesDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService
setProcessingSamplesDAO.
setProcessingSamplesId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
Setter for the field processingSamplesId.
setProcessingSamplesService(ProcessingSamplesService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field processingSamplesService.
setProcessingSequencerRunsDAO(ProcessingSequencerRunsDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
setProcessingSequencerRunsDAO.
setProcessingSequencerRunsDAO(ProcessingSequencerRunsDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService
setProcessingSequencerRunsDAO.
setProcessingSequencerRunService(ProcessingSequencerRunsService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field processingSequencerRunService.
setProcessingSequencerRunsId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
Setter for the field processingSequencerRunsId.
setProcessingService(ProcessingService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
Setter for the field processingService.
setProcessingsForView(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Lane
setProcessingsForView.
setProcessingStudiesDAO(ProcessingStudiesDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
setProcessingStudiesDAO.
setProcessingStudiesDAO(ProcessingStudiesDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService
setProcessingStudiesDAO.
setProcessingStudiesId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
Setter for the field processingStudiesId.
setProcessingStudiesService(ProcessingStudiesService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field processingStudiesService.
setProjectDAO(ProjectDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
setProjectDAO.
setProjectDAO(ProjectDAO) - Method in interface net.sourceforge.seqware.common.business.ProjectService
setProjectDAO.
setProjectId(Integer) - Method in class net.sourceforge.seqware.common.model.Project
Setter for the field projectId.
setProjectId(Integer) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field projectId.
setPROJECTID(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Sets the value of the projectid property.
setPROTECT(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Sets the value of the protect property.
setPublic(boolean) - Method in class net.sourceforge.seqware.common.model.Workflow
setPublic.
setQCREPORT(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Sets the value of the qcreport property.
setQtype(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
Sets the value of the qtype property.
setQualityMultiplier(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field qualityMultiplier.
setQualityNumberOfLevels(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field qualityNumberOfLevels.
setQualityScorer(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field qualityScorer.
setQUALITYSCORER(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
Sets the value of the qualityscorer property.
setQualityType(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field qualityType.
setQueue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
setQueue(String) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
set the queue
setRandom(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
set the pre-defined random variable
setReadBases(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field readBases.
setReadClass(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Setter for the field readClass.
setREADCLASS(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Sets the value of the readclass property.
setReadCount(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field readCount.
setReader(BufferedReader) - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
Setter for the field reader.
setReadIndex(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Setter for the field readIndex.
setREADINDEX(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Sets the value of the readindex property.
setReadLabel(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Setter for the field readLabel.
setReadOnly(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field readOnly.
setReadSpec(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
Setter for the field readSpec.
setReadSpecs(SortedSet<ExperimentSpotDesignReadSpec>) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
Setter for the field readSpecs.
setReadsPerSpot(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
Setter for the field readsPerSpot.
setReadsSupportingCallOne(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field readsSupportingCallOne.
setReadsSupportingCallThree(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field readsSupportingCallThree.
setReadsSupportingCallTwo(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field readsSupportingCallTwo.
setReadType(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
Setter for the field readType.
setREADTYPE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
Sets the value of the readtype property.
setReadyToProcess(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
setReadyToProcess.
setReadyToProcess(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field readyToProcess.
setReference(Reference) - Method in class com.github.seqware.queryengine.model.FeatureSet.Builder
 
setReference(Reference) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet.Builder
 
setReference(Reference) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.Builder
 
setReferenceACL(ACL, Reference) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
setReferenceACL.
setREFERENCEALIGNMENT(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Sets the value of the referencealignment property.
setReferenceAveSeqQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field referenceAveSeqQuality.
setReferenceBase(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field referenceBase.
setReferenceCallQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field referenceCallQuality.
setReferenceID(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setReferenceID(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
 
setReferenceID(SGID) - Method in class com.github.seqware.queryengine.model.FeatureSet.Builder
 
setReferenceID(SGID) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet.Builder
 
setReferenceID(SGID) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.Builder
 
setReferenceId(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field referenceId.
setReferenceIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setReferenceIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
 
setReferenceMaxSeqQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field referenceMaxSeqQuality.
setReferenceSetACL(ACL, ReferenceSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
setReferenceSetACL.
setRefLane(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field refLane.
setRefLane(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field refLane.
setRefName(String) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF
Sets the value of the refname property.
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF
Sets the value of the refname property.
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF
Sets the value of the refname property.
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF
Sets the value of the refname property.
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR
Sets the value of the refname property.
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF
Sets the value of the refname property.
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF
Sets the value of the refname property.
setRegion(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Sets the value of the region property.
setRegions(String) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field regions.
setRegions(String) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field regions.
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
Setter for the field registration.
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareFile
Setter for the field registration.
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareLane
Setter for the field registration.
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
Setter for the field registration.
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareSample
Setter for the field registration.
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareStudy
Setter for the field registration.
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
Setter for the field registration.
setRegistrationDAO(RegistrationDAO) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
setRegistrationDAO.
setRegistrationDAO(RegistrationDAO) - Method in interface net.sourceforge.seqware.common.business.RegistrationService
setRegistrationDAO.
setRegistrationId(Integer) - Method in class net.sourceforge.seqware.common.model.Registration
Setter for the field registrationId.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field registrationService.
setRegistrationService(RegistrationService) - Static method in class net.sourceforge.seqware.webservice.resources.BasicResource
Setter for the field registrationService.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
Setter for the field registrationService.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
Setter for the field registrationService.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController
Setter for the field registrationService.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.LoginController
Setter for the field registrationService.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
Setter for the field registrationService.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController
Setter for the field registrationService.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
Setter for the field registrationService.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.SignUpController
Setter for the field registrationService.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Setter for the field registrationService.
setRelationship(String) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship
Setter for the field relationship.
setRelativeLocation(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field relativeLocation.
setRELEASE(SubmissionType.ACTIONS.ACTION.RELEASE) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Sets the value of the release property.
setReportInputFiles(boolean) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
 
setRequireFiles(boolean) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Setter for the field requireFiles.
setRequirements(Collection<Requirement>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
setReturnIds(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field returnIds.
setReturnValue(ReturnValue) - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException
Setter for the field returnValue.
setReturnValue(int) - Method in class net.sourceforge.seqware.common.module.ReturnValue
Setter for the field returnValue.
setRights(int, boolean) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
setRights(boolean[]) - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder
 
setRights(List<Boolean>) - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder
 
setRootProcessingName(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setRootProcessingSwa(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setRootSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
Setter for the field rootSample.
setRowId(Integer) - Method in class net.sourceforge.seqware.common.model.FileReportRow
Setter for the field rowId.
setRowId(Integer) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
Setter for the field rowId.
setRowKey(String) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
setRows(List<Flexigrid.Cells>) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
Setter for the field rows.
setRUNATTRIBUTES(RunType.RUNATTRIBUTES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the runattributes property.
setRunCenter(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field runCenter.
setRunCenter(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field runCenter.
setRunCenter(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the runCenter property.
setRunDate(XMLGregorianCalendar) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the runDate property.
setRunFile(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the runFile property.
setRUNLINKS(RunType.RUNLINKS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the runlinks property.
setRunName(String) - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.Header
Set the value of runName
setRUNREF(AnalysisType.PARENT.RUNREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Sets the value of the runref property.
setRunStartTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field runStartTimestamp.
setRunStartTstmp(Date) - Method in class net.sourceforge.seqware.common.module.ReturnValue
Setter for the field runStartTstmp.
setRunStopTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field runStopTimestamp.
setRunStopTstmp(Date) - Method in class net.sourceforge.seqware.common.module.ReturnValue
Setter for the field runStopTstmp.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.FileReportRow
Setter for the field sample.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.IUS
Setter for the field sample.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field sample.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
Setter for the field sample.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
Setter for the field sample.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleLink
Setter for the field sample.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleSearch
Setter for the field sample.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.ShareSample
Setter for the field sample.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.UploadSequence
Setter for the field sample.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Setter for the field sample.
setSample(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
setSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Setter for the field sample.
setSample_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Setter for the field sample_url.
setSampleAttributeId(int) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
Setter for the field sampleAttributeId.
setSampleAttributes(Set<SampleAttribute>) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field sampleAttributes.
setSAMPLEATTRIBUTES(SampleType.SAMPLEATTRIBUTES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Sets the value of the sampleattributes property.
setSampleCode(String) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field sampleCode.
setSampleDAO(SampleDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
Setter for the field sampleDAO.
setSampleDAO(SampleDAO) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
setSampleDAO.
setSampleDAO(SampleDAO) - Method in interface net.sourceforge.seqware.common.business.SampleService
setSampleDAO.
setSAMPLEDESCRIPTOR(ExperimentType.DESIGN.SAMPLEDESCRIPTOR) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
Sets the value of the sampledescriptor property.
setSampleForStudy(Sample, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setSampleForStudy.
setSampleForWorkflowRun(Sample, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setSampleForWorkflowRun.
setSampleForWorkflowRunRunning(Sample, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setSampleForWorkflowRunRunning.
setSampleHierarchies(List<SampleHierarchy>) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchies
 
setSampleId(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field sampleId.
setSampleId(Integer) - Method in class net.sourceforge.seqware.common.model.UploadSequence
Setter for the field sampleId.
setSampleId(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
Sets the value of the sampleId property.
setSampleId(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleHierarchy
 
setSampleId(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
Sets the value of the sampleId property.
setSampleId(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto
Setter for the field sampleId.
setSampleLinkId(int) - Method in class net.sourceforge.seqware.common.model.SampleLink
Setter for the field sampleLinkId.
setSampleLinks(Set<SampleLink>) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field sampleLinks.
setSAMPLELINKS(SampleType.SAMPLELINKS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Sets the value of the samplelinks property.
setSAMPLENAME(SampleType.SAMPLENAME) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
Sets the value of the samplename property.
setSAMPLEPOOLREF(AnalysisType.PARENT.SAMPLEPOOLREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Sets the value of the samplepoolref property.
setSampleRef(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
Sets the value of the sampleRef property.
setSAMPLEREF(AnalysisType.PARENT.SAMPLEREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Sets the value of the sampleref property.
setSampleRef(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
Sets the value of the sampleRef property.
setSampleReportDAO(SampleReportDAO) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
Setter for the field sampleReportDAO.
setSampleReportService(SampleReportService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field sampleReportService.
setSampleReportService(SampleReportService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Setter for the field sampleReportService.
setSampleReportService(SampleReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
Setter for the field sampleReportService.
setSampleReportService(SampleReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Setter for the field sampleReportService.
setSamples(SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field samples.
setSamples(Set<Sample>) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field samples.
setSamples(SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.model.Project
Setter for the field samples.
setSamples(SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field samples.
setSamples(List<BatchMetadataInjection.SampleInfo>) - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.RunInfo
 
setSampleSearch(SampleSearch) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
Setter for the field sampleSearch.
setSampleSearchAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
Setter for the field sampleSearchAttributeId.
setSampleSearchAttributes(Set<SampleSearchAttribute>) - Method in class net.sourceforge.seqware.common.model.SampleSearch
Setter for the field sampleSearchAttributes.
setSampleSearchId(Integer) - Method in class net.sourceforge.seqware.common.model.SampleSearch
Setter for the field sampleSearchId.
setSampleService(SampleService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.validation.SampleValidator
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
Setter for the field sampleService.
setSampleSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setSampleType(String) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field sampleType.
setSampleUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto
Setter for the field sampleUrl.
setSchema(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
Sets the value of the schema property.
setSchema(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
Sets the value of the schema property.
setScore(double) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setScore(Double) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setScore(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Setter for the field score.
setSector(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Sets the value of the sector property.
setSelection(LibrarySelection) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Setter for the field selection.
setSender(MailSender) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
Setter for the field sender.
setSeqid(String) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setSequencer_run_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Setter for the field sequencer_run_url.
setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field sequencerRun.
setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
Setter for the field sequencerRun.
setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
Setter for the field sequencerRun.
setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
Setter for the field sequencerRun.
setSequencerRun(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
setSequencerRun(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setSequencerRun.
setSequencerRunAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
Setter for the field sequencerRunAttributeId.
setSequencerRunAttributes(Set<SequencerRunAttribute>) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field sequencerRunAttributes.
setSequencerRunDAO(SequencerRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
Setter for the field sequencerRunDAO.
setSequencerRunDAO(SequencerRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
setSequencerRunDAO.
setSequencerRunDAO(SequencerRunDAO) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
setSequencerRunDAO.
setSequencerRunId(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field sequencerRunId.
setSequencerRunId(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field sequencerRunId.
setSequencerRuns(Set<SequencerRun>) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field sequencerRuns.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListController
Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportSetupController
Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController
Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO
Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
Setter for the field sequencerRunService.
setSequencerRunSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setSequencerRunValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Setter for the field sequencerRunValidator.
setSequencerRunWizardDTO(SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
setSequencerRunWizardDTO.
setSequencerRunWizardValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController
Setter for the field sequencerRunWizardValidator.
setSequenceSpace(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field sequenceSpace.
setSEQUENCESPACE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS
Sets the value of the sequencespace property.
setSEQUENCINGPROTOCOL(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Sets the value of the sequencingprotocol property.
setSeqwareAccession(Integer) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
setSeqwareAccessionString(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
setSeqwareRevision(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field seqwareRevision.
setSeqwareVersion(String) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field seqwareVersion.
setSerializationConstant(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
setSerializationConstant(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
setServer(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field server.
setSessionFactory(SessionFactory) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field sessionFactory.
setSettings(SeqWareSettings) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
setSettings.
setSettings(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
setSettings.
setSettings(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
setSettings.
setSettings(SeqWareSettings) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
setSettings.
setSETTINGS_MAP(Map<String, String>) - Static method in class com.github.seqware.queryengine.Constants
Set the settings map, overriding hard-coded values for our constants.
setSgid(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
setSgid(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
setSgid(QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
setSgid(QESupporting.FSGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
setSgid(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
setSgid(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
setSGID(SGID) - Method in class com.github.seqware.queryengine.util.LazyReference
Set the SGID of the object to be lazy referenced
setSharedStudies(SortedSet<ShareStudy>) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field sharedStudies.
setSharedWorkflowRuns(SortedSet<ShareWorkflowRun>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field sharedWorkflowRuns.
setShareExperimentDAO(ShareExperimentDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
setShareExperimentDAO.
setShareExperimentDAO(ShareExperimentDAO) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
setShareExperimentDAO.
setShareExperimentId(int) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
Setter for the field shareExperimentId.
setShareFileDAO(ShareFileDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
setShareFileDAO.
setShareFileDAO(ShareFileDAO) - Method in interface net.sourceforge.seqware.common.business.ShareFileService
setShareFileDAO.
setShareFileId(int) - Method in class net.sourceforge.seqware.common.model.ShareFile
Setter for the field shareFileId.
setShareLaneDAO(ShareLaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
setShareLaneDAO.
setShareLaneDAO(ShareLaneDAO) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
setShareLaneDAO.
setShareLaneId(int) - Method in class net.sourceforge.seqware.common.model.ShareLane
Setter for the field shareLaneId.
setShareProcessingDAO(ShareProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
setShareProcessingDAO.
setShareProcessingDAO(ShareProcessingDAO) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
setShareProcessingDAO.
setShareProcessingId(int) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
Setter for the field shareProcessingId.
setShareSampleDAO(ShareSampleDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
setShareSampleDAO.
setShareSampleDAO(ShareSampleDAO) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
setShareSampleDAO.
setShareSampleId(int) - Method in class net.sourceforge.seqware.common.model.ShareSample
Setter for the field shareSampleId.
setShareStudyDAO(ShareStudyDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
setShareStudyDAO.
setShareStudyDAO(ShareStudyDAO) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
setShareStudyDAO.
setShareStudyId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareStudy
Setter for the field shareStudyId.
setShareStudyService(ShareStudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
Setter for the field shareStudyService.
setShareStudyService(ShareStudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Setter for the field shareStudyService.
setShareWorkflowRunDAO(ShareWorkflowRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
setShareWorkflowRunDAO.
setShareWorkflowRunDAO(ShareWorkflowRunDAO) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
setShareWorkflowRunDAO.
setShareWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
Setter for the field shareWorkflowRunId.
setShareWorkflowRunService(ShareWorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
Setter for the field shareWorkflowRunService.
setShareWorkflowRunService(ShareWorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
Setter for the field shareWorkflowRunService.
setSINGLE(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
Sets the value of the single property.
setSite(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn
Setter for the field site.
setSize(Long) - Method in class net.sourceforge.seqware.common.model.File
Setter for the field size.
setSize(Long) - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
setSize(Long) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
setSize(Long) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
Setter for the field size.
setSizeString(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.IUS
Setter for the field skip.
setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field skip.
setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field skip.
setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field skip.
setSkip(Boolean) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Setter for the field skip.
setSkipTxt(String) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field skipTxt.
setSlideOneFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field slideOneFilePath.
setSlideOneFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field slideOneFilePath.
setSlideOneLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field slideOneLaneCount.
setSlideOneLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field slideOneLaneCount.
setSlideTwoFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field slideTwoFilePath.
setSlideTwoFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field slideTwoFilePath.
setSlideTwoLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field slideTwoLaneCount.
setSlideTwoLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field slideTwoLaneCount.
setSortable(boolean) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
setSortKeySample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Setter for the field sortKeySample.
setSource(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setSource(String) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setSource(LibrarySource) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Setter for the field source.
setSource(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Setter for the field source.
setSource(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
Sets the value of the source property.
setSource(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
Sets the value of the source property.
setSource(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
Sets the value of the source property.
setSourcePath(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
 
setSPOTDECODEMETHOD(Long) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR
Sets the value of the spotdecodemethod property.
setSPOTDECODESPEC(ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR
Sets the value of the spotdecodespec property.
setSPOTDESCRIPTOR(ExperimentType.DESIGN.SPOTDESCRIPTOR) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
Sets the value of the spotdescriptor property.
setSpotDesignReadSpec(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field spotDesignReadSpec.
setSql(Statement) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
Setter for the field sql.
setStart(long) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setStart(long) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setStart(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
Setter for the field start.
setStartDate(Date) - Method in class net.sourceforge.seqware.common.model.Invoice
Setter for the field startDate.
setStartPage(String) - Method in class net.sourceforge.solexatools.util.PageInfo
Setter for the field startPage.
setStartPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.ContigPosition
Setter for the field startPosition.
setStartPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
Setter for the field startPosition.
setStartPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field startPosition.
setState(CreateUpdateManager.State) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager.AtomStatePair
 
setState(String) - Method in class net.sourceforge.seqware.common.model.Invoice
Setter for the field state.
setStats(HashMap) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
Setter for the field stats.
setStatus(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field status.
setStatus(String) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field status.
setStatus(String) - Method in class net.sourceforge.seqware.common.model.Project
Setter for the field status.
setStatus(String) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
Setter for the field status.
setStatus(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field status.
setStatus(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field status.
setStatus(String) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field status.
setStatus(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field status.
setStatusCmd(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field statusCmd.
setStatusCounts(int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
Setter for the field statusCounts.
setStatuses(String[]) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Setter for the field statuses.
setStderr(String) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field stderr.
setStdErr(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field stdErr.
setStderr(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
Setter for the field stderr.
setStderr(File) - Method in interface net.sourceforge.seqware.pipeline.module.RedirectAware
setStderr.
setStderrFile(File) - Method in class net.sourceforge.seqware.pipeline.module.Module
Added by Xiaoshu Wang: Setter for the file that will be used to redirect stderr
setStdout(String) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field stdout.
setStdOut(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field stdOut.
setStdout(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
Setter for the field stdout.
setStdout(File) - Method in interface net.sourceforge.seqware.pipeline.module.RedirectAware
setStdout.
setStdoutFile(File) - Method in class net.sourceforge.seqware.pipeline.module.Module
Setter for the field stdoutFile.
setStop(long) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setStop(long) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setStop(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
Setter for the field stop.
setStopPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.ContigPosition
Setter for the field stopPosition.
setStopPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
Setter for the field stopPosition.
setStopPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field stopPosition.
setStore(Store) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Setter for the field store.
setStore(BerkeleyDBStore) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
Setter for the field store.
setStore(Store) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Setter for the field store.
setStoreType(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field storeType.
setStrand(QueryEngine.FeaturePB.StrandPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setStrand(Feature.Strand) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setStrand(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Setter for the field strand.
setStrand(char) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Setter for the field strand.
setStrategy(LibraryStrategy) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
Setter for the field strategy.
setStrExpectedNumberReads(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field strExpectedNumberReads.
setStrExpectedNumberRuns(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field strExpectedNumberRuns.
setStrExpectedNumReads(String) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field strExpectedNumReads.
setStrExpectedNumRuns(String) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field strExpectedNumRuns.
setStrLaneCount(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO
Setter for the field strLaneCount.
setStrRefLane(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field strRefLane.
setStrStartURL(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
Setter for the field strStartURL.
setStrStartURL(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
Setter for the field strStartURL.
setStudies(Set<Study>) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field studies.
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field study.
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.FileReportRow
Setter for the field study.
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
Setter for the field study.
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
Setter for the field study.
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId
Setter for the field study.
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
Setter for the field study.
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.StudyLink
Setter for the field study.
setStudy(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setStudy.
setSTUDYABSTRACT(JAXBElement<String>) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Sets the value of the studyabstract property.
setStudyAttributeId(int) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
Setter for the field studyAttributeId.
setStudyAttributes(Set<StudyAttribute>) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field studyAttributes.
setSTUDYATTRIBUTES(StudyType.STUDYATTRIBUTES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Sets the value of the studyattributes property.
setStudyDAO(StudyDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
Setter for the field studyDAO.
setStudyDAO(StudyDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
setStudyDAO.
setStudyDAO(StudyDAO) - Method in interface net.sourceforge.seqware.common.business.StudyService
setStudyDAO.
setSTUDYDESCRIPTION(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Sets the value of the studydescription property.
setStudyId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareStudy
Setter for the field studyId.
setStudyId(Integer) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field studyId.
setStudyLinkId(int) - Method in class net.sourceforge.seqware.common.model.StudyLink
Setter for the field studyLinkId.
setStudyLinks(Set<StudyLink>) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field studyLinks.
setSTUDYLINKS(StudyType.STUDYLINKS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
Sets the value of the studylinks property.
setSTUDYREF(AnalysisType.PARENT.STUDYREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
Sets the value of the studyref property.
setSTUDYREF(ExperimentType.STUDYREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the studyref property.
setStudyService(StudyService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.validation.StudyValidator
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportSetupController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
Setter for the field studyService.
setStudySwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
setStudyTitle(String) - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.Header
Set the value of studyTitle
setSTUDYTITLE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Sets the value of the studytitle property.
setStudyType(StudyType) - Method in class net.sourceforge.seqware.common.model.Lane
 
setSTUDYTYPE(StudyType.DESCRIPTOR.STUDYTYPE) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
Sets the value of the studytype property.
setStudyTypeDAO(StudyTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
Setter for the field studyTypeDAO.
setStudyTypeDAO(StudyTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
setStudyTypeDAO.
setStudyTypeDAO(StudyTypeDAO) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService
setStudyTypeDAO.
setStudyTypeId(Integer) - Method in class net.sourceforge.seqware.common.model.StudyType
Setter for the field studyTypeId.
setStudyTypeService(StudyTypeService) - Method in class net.sourceforge.seqware.common.ContextImpl
 
setStudyTypeService(StudyTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
Setter for the field studyTypeService.
setStudyTypeService(StudyTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
Setter for the field studyTypeService.
setSubmissionComment(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the submissionComment property.
setSubmissionDate(XMLGregorianCalendar) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the submissionDate property.
setSubmissionId(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the submissionId property.
setSum(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage
Setter for the field sum.
setSummaryLines(List<SummaryLine>) - Method in class net.sourceforge.solexatools.util.SummaryData
Setter for the field summaryLines.
setSUPPRESS(SubmissionType.ACTIONS.ACTION.SUPPRESS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Sets the value of the suppress property.
setSvType(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field svType.
setSwa(Integer) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Setter for the field swa.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Expense
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.File
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Invoice
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.IUS
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareFile
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareLane
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareSample
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareStudy
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field swAccession.
setSwCluster(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
 
setTag(String) - Method in interface net.sourceforge.seqware.common.model.Attribute
setTag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
Setter for the field tag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.FileAttribute
setTag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.IUS
Setter for the field tag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
setTag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
Setter for the field tag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
setTag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
setTag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
setTag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
setTag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
setTag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
setTag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
setTag.
setTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Tag
Setter for the field tag.
setTAG(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
Sets the value of the tag property.
setTAG(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
Sets the value of the tag property.
setTAG(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
Sets the value of the tag property.
setTAG(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
Sets the value of the tag property.
setTAG(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
Sets the value of the tag property.
setTagACL(ACL, Tag) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
setTagACL.
setTags(int, QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
setTags(int, QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
 
setTags(int, QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
setTags(int, QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
 
setTags(String) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field tags.
setTags(String) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field tags.
setTags(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
set the key-value properties from metadata.xml
setTags(HashMap<String, String>) - Method in class net.sourceforge.seqware.queryengine.backend.model.Model
setTags.
setTags(HashMap<String, String>) - Method in interface net.sourceforge.seqware.queryengine.backend.model.ModelInterface
setTags.
setTags(HashMap<String, String>) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
setTags.
setTagSet(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setTagSet(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setTagSet(TagSet) - Method in class com.github.seqware.queryengine.model.Tag.Builder
 
setTagSet(SGID) - Method in class com.github.seqware.queryengine.model.Tag.Builder
 
setTagSet(SGID) - Method in class com.github.seqware.queryengine.model.Tag
Set the TagSet for this particular tag, should not be called outside of the back-end.
setTagSet(TagSet) - Method in class com.github.seqware.queryengine.model.Tag
Set the TagSet for this particular tag, should not be called outside of the back-end.
setTagSetACL(ACL, TagSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
setTagSetACL.
setTagSetIDs(List<SGID>) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Setter for the field tagSetIDs.
setTagSpec(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
Setter for the field tagSpec.
setTagSpecIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
setTagSpecIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
 
setTarget(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
Sets the value of the target property.
setTarget(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
Sets the value of the target property.
setTarget(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE
Sets the value of the target property.
setTarget(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS
Sets the value of the target property.
setTargetedResequencing(String) - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Set the value of targetedResequencing
setTaskGroup(boolean) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field taskGroup.
setTAXONID(Integer) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
Sets the value of the taxonid property.
setTemplate(String) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field template.
setTemplate(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field template.
setTemplateFile(String) - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
Setter for the field templateFile.
setTemplatePath(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Setter for the field templatePath.
setTemplateType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Set the value of templateType
setTemplateType(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
Setter for the field templateType.
setTest(Boolean) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
setTestCmd(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Setter for the field testCmd.
setThickEnd(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Setter for the field thickEnd.
setThickStart(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Setter for the field thickStart.
setThreads(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
 
setThreads(int) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
set the max thread number
setTimestamp(long) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
 
setTimestamp(Date) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
Set the clientTimestamp, this should never be called outside of the backend
setTimeTaken(String) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
Setter for the field timeTaken.
SETTINGSFILENOTFOUND - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant SETTINGSFILENOTFOUND=13
setTissSource(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
Setter for the field tissSource.
setTissueOrigin(String) - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Set the value of tissueOrigin
setTissuePreparation(String) - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Set the value of tissuePreparation
setTissueRegion(String) - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Set the value of tissueRegion
setTissueType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
Set the value of tissueType
setTitle(String) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field title.
setTitle(String) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field title.
setTitle(String) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field title.
setTITLE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
Sets the value of the title property.
setTITLE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Sets the value of the title property.
setTITLE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Sets the value of the title property.
setTombstone(boolean) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
 
setTombstone(boolean) - Method in class com.github.seqware.queryengine.util.FSGID
Back-end method for Features stored within high capacity featuresets
setTotal(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid
Setter for the field total.
setTotalDataBlocks(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType
Sets the value of the totalDataBlocks property.
setTotalPrice(Double) - Method in class net.sourceforge.seqware.common.model.Expense
Setter for the field totalPrice.
setTotalReads(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Sets the value of the totalReads property.
setTotalSpots(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Sets the value of the totalSpots property.
setTotalUnits(Double) - Method in class net.sourceforge.seqware.common.model.Expense
Setter for the field totalUnits.
setTRANSCRIPTASSEMBLY(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Sets the value of the transcriptassembly property.
setTranscriptId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature
Setter for the field transcriptId.
setTRANSCRIPTSEQUENCING(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
Sets the value of the transcriptsequencing property.
setTranslatedSequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence
Setter for the field translatedSequence.
setTranslocationDestinationContig(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field translocationDestinationContig.
setTranslocationDestinationStartPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field translocationDestinationStartPosition.
setTranslocationDestinationStopPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field translocationDestinationStopPosition.
setTranslocationType(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field translocationType.
setTreeAdaptor(TreeAdaptor) - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
setTreeAdaptor.
setTTL(long, boolean) - Method in class com.github.seqware.queryengine.model.impl.AbstractMolSet
Convenience method to set the expiry time
setTTL(int, boolean) - Method in class com.github.seqware.queryengine.model.impl.AbstractMolSet
Convenience method to set the expiry time for roughly hours ahead
setTTL(long, boolean) - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl
Convenience method to set the expiry time
setTTL(int, boolean) - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl
Convenience method to set the expiry time for roughly hours ahead
setTTL(long, boolean) - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable
Convenience method to set the expiry time
setTTL(int, boolean) - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable
Convenience method to set the expiry time for roughly hours ahead
setType(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
 
setType(String) - Method in class com.github.seqware.queryengine.model.Feature.Builder
 
setType(String) - Method in class net.sourceforge.seqware.common.model.File
Setter for the field type.
setType(String) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field type.
setType(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence
Setter for the field type.
setType(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Setter for the field type.
setType(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
Setter for the field type.
setType(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
setType(Requirement.Type) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
 
setType(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
 
setType(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field type.
setType(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
Setter for the field type.
setType(String) - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
Setter for the field type.
setTypeNode(String) - Method in class net.sourceforge.seqware.common.business.UploadFile
Setter for the field typeNode.
setUnit(String) - Method in interface net.sourceforge.seqware.common.model.Attribute
setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.common.model.FileAttribute
setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
Setter for the field unit.
setUnits(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
Setter for the field units.
setUnits(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
Setter for the field units.
setUnits(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
Setter for the field units.
setUnits(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
Setter for the field units.
setUnits(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
Setter for the field units.
setUnits(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
Setter for the field units.
setUnits(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
Setter for the field units.
setUNITS(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
Sets the value of the units property.
setUNITS(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
Sets the value of the units property.
setUNITS(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
Sets the value of the units property.
setUNITS(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
Sets the value of the units property.
setUNITS(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
Sets the value of the units property.
setup(Mapper.Context) - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner.PluginRunnerMapper
 
setup(String) - Static method in class net.sourceforge.seqware.common.util.freemarker.Freemarker
setup.
setup(SeqWareSettings) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
setup.
setup(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
setup.
setup(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
setup.
setup(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
setup.
setup(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
setup.
setup(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
setup.
setup(SeqWareSettings) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
setup.
setup(String) - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
This allows you to search for different types of data in the metadb not just query engine databases
setup() - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
setup.
setup(ArrayList) - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
setup.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Experiment
Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.IUS
Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Project
Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Registration
Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Sample
Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareStudy
Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Study
Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field updateTimestamp.
setUpdateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Setter for the field updateTimeStamp.
setUpdateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Setter for the field updateTimeStamp.
setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareExperiment
Setter for the field updateTstmp.
setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareFile
Setter for the field updateTstmp.
setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareLane
Setter for the field updateTstmp.
setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareProcessing
Setter for the field updateTstmp.
setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareSample
Setter for the field updateTstmp.
setUpdateValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Setter for the field updateValidator.
setUpdateValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
setUpdateValidator.
setupDirectory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
to be Overridden by the workflow author
setupEnvironment() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
to be Overridden by the workflow author generally people don't override this.
setupFiles() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
to be Overridden by the workflow author the place to specify inputs and outputs to the program also, a user can specify inputs and outputs on jobs directly in which case they are still provisioned properly with respect to the job (inputs before, outputs after) when you define inputs/outputs here they are provisioned before all jobs and after all jobs respectively
setupWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
to be Overridden by the workflow author you generally don't call this as the workflow author since it promotes hardcoding this will typically be filled in by maven
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink
Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.File
Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.IUSLink
Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.LaneLink
Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments
Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingIus
Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes
Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples
Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns
Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies
Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.SampleLink
Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.StudyLink
Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
setUrl(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn
Setter for the field url.
setURL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
Sets the value of the url property.
setURL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
Sets the value of the url property.
setURL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK
Sets the value of the url property.
setURL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
Sets the value of the url property.
setURL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK
Sets the value of the url property.
setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto
Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto
Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto
Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto
Setter for the field url.
setUrlLabel(String) - Method in class net.sourceforge.seqware.common.model.File
Setter for the field urlLabel.
setUrlLabel(String) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field urlLabel.
setUrlLabel(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
setUrlLabel(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
Setter for the field urlLabel.
setURLLINK(AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
Sets the value of the urllink property.
setURLLINK(ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
Sets the value of the urllink property.
setURLLINK(RunType.RUNLINKS.RUNLINK.URLLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK
Sets the value of the urllink property.
setURLLINK(SampleType.SAMPLELINKS.SAMPLELINK.URLLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK
Sets the value of the urllink property.
setURLLINK(StudyType.STUDYLINKS.STUDYLINK.URLLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK
Sets the value of the urllink property.
setUrlString(String) - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
Setter for the field urlString.
setUseIparIntensities(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun
Setter for the field useIparIntensities.
setUseIparIntensities(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
Setter for the field useIparIntensities.
setUseOneURL(Boolean) - Method in class net.sourceforge.seqware.common.model.UploadSequence
Setter for the field useOneURL.
setUser(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
setUser(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
 
setUsername(String) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field username.
setUserName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field userName.
setUsername(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
Setter for the field username.
setUsers(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setUsers(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
 
setUseTwoURL(Boolean) - Method in class net.sourceforge.seqware.common.model.UploadSequence
Setter for the field useTwoURL.
setUseURL(Boolean) - Method in class net.sourceforge.seqware.common.business.UploadFile
Setter for the field useURL.
setUuid(UUID) - Method in class com.github.seqware.queryengine.util.SGID
Setter for the field uuid.
setVALIDATE(SubmissionType.ACTIONS.ACTION.VALIDATE) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
Sets the value of the validate property.
setValidationReportService(ValidationReportService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field validationReportService.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.FileController
Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController
Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController
Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController
Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController
Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController
Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO
Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController
setValidator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController
Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
Setter for the field validator.
setValue(Object) - Method in class com.github.seqware.queryengine.model.Tag.Builder
Set the value to one of ValueType
setValue(String) - Method in interface net.sourceforge.seqware.common.model.Attribute
setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
Setter for the field value.
setValue(String) - Method in class net.sourceforge.seqware.common.model.FileAttribute
setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
Setter for the field value.
setValue(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute
setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Setter for the field value.
setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
Setter for the field value.
setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
Setter for the field value.
setValue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
Setter for the field value.
setValue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile
Setter for the field value.
setValue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
 
setValue(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Tag
Setter for the field value.
setVALUE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
Sets the value of the value property.
setVALUE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
Sets the value of the value property.
setValue(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
Sets the value of the value property.
setVALUE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
Sets the value of the value property.
setVALUE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
Sets the value of the value property.
setVALUE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
Sets the value of the value property.
setValue(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto
Setter for the field value.
setValues(SortedSet<WorkflowParamValue>) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Setter for the field values.
setVBytes(ByteString) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setVDouble(double) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setVerbose(boolean) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
Enable class verbose mode.
setVerbose(boolean) - Static method in class net.sourceforge.seqware.common.util.Log
override the log4j.properties
setVersion(String) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field version.
setVersion(String) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field version.
setVersion(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue
Setter for the field version.
setVersion(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Setter for the field version.
setVersion(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
set workflow version
setVersion(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
 
setVFloat(float) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setVInteger(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setVisibleParams(SortedSet<WorkflowParam>) - Method in class net.sourceforge.solexatools.util.SummaryData
Setter for the field visibleParams.
setVLong(long) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setVSGIDRef(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setVSGIDRef(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setVString(String) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
 
setWait(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
wait for the workflow to finished, user can override this by using --wait from command line
setWfRuns(WorkflowRun[]) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Setter for the field wfRuns.
setWidth(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
 
setWithHasFile(SortedSet<Experiment>) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
setWithHasFile.
setWithHasFile(Set<File>, String) - Method in interface net.sourceforge.seqware.common.business.FileService
setWithHasFile.
setWithHasFile(SortedSet<Experiment>) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
setWithHasFile.
setWithHasFile(Set<File>, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
setWithHasFile.
setWithHasFile(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
setWithHasFile.
setWithHasFile(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
setWithHasFile.
setWithHasFile(Set<Processing>) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
setWithHasFile.
setWithHasFile(Set<Processing>, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
setWithHasFile.
setWithHasFile(Integer, SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
setWithHasFile.
setWithHasFile(SortedSet<IUS>) - Method in interface net.sourceforge.seqware.common.business.IUSService
setWithHasFile.
setWithHasFile(SortedSet<Lane>) - Method in interface net.sourceforge.seqware.common.business.LaneService
setWithHasFile.
setWithHasFile(Set<Processing>) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
setWithHasFile.
setWithHasFile(Set<Processing>, String) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
setWithHasFile.
setWithHasFile(Integer, SortedSet<Sample>) - Method in interface net.sourceforge.seqware.common.business.SampleService
setWithHasFile.
setWorkerName(String) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Setter for the field workerName.
setWorkerName(String) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker
Setter for the field workerName.
setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.SampleReportRow
Setter for the field workflow.
setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
Setter for the field workflow.
setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Setter for the field workflow.
setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field workflow.
setWorkflowAccession(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setWorkflowAccession(int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Setter for the field workflowAccession.
setWorkflowAccession(String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
setWorkflowAccessionsToCheck(Set<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
setWorkflowAttributes(Set<WorkflowAttribute>) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field workflowAttributes.
setWorkflowBundleDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
 
setWorkflowBundleDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
set the workflowBundle directory
setWorkflowClass(String) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setWorkflowClass(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setWorkflowDAO(WorkflowDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
setWorkflowDAO.
setWorkflowDAO(WorkflowDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
setWorkflowDAO.
setWorkflowDir(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
Setter for the field workflowDir.
setWorkflowEngine(String) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setWorkflowEngine(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
 
setWorkflowEngine(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setWorkflowId(Integer) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field workflowId.
setWorkflowParam(WorkflowParam) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
Setter for the field workflowParam.
setWorkflowParamDAO(WorkflowParamDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
setWorkflowParamDAO.
setWorkflowParamDAO(WorkflowParamDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
setWorkflowParamDAO.
setWorkflowParamId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
Setter for the field workflowParamId.
setWorkflowParamId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
Setter for the field workflowParamId.
setWorkflowParams(SortedSet<WorkflowParam>) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field workflowParams.
setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field workflowParamService.
setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
Setter for the field workflowParamService.
setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController
Setter for the field workflowParamService.
setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
Setter for the field workflowParamService.
setWorkflowParamValueDAO(WorkflowParamValueDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
setWorkflowParamValueDAO.
setWorkflowParamValueDAO(WorkflowParamValueDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
setWorkflowParamValueDAO.
setWorkflowParamValueId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
Setter for the field workflowParamValueId.
setWorkflowParamValueService(WorkflowParamValueService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field workflowParamValueService.
setWorkflowParamValueService(WorkflowParamValueService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
Setter for the field workflowParamValueService.
setWorkflowParamValueService(WorkflowParamValueService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
Setter for the field workflowParamValueService.
setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
Setter for the field workflowRun.
setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.Expense
Setter for the field workflowRun.
setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field workflowRun.
setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
Setter for the field workflowRun.
setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
Setter for the field workflowRun.
setWorkflowRun(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setWorkflowRun.
setWorkflowRunAccession(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
setWorkflowRunAccession(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
setWorkflowRunAncesstor(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
setWorkflowRunAncesstor(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
setWorkflowRunAttributes(Set<WorkflowRunAttribute>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field workflowRunAttributes.
setWorkflowRunByAncestorWorkflowRunId(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field workflowRunByAncestorWorkflowRunId.
setWorkflowRunDAO(WorkflowRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
setWorkflowRunDAO.
setWorkflowRunDAO(WorkflowRunDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
setWorkflowRunDAO.
setWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.Processing
Setter for the field workflowRunId.
setWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
Setter for the field workflowRunId.
setWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field workflowRunId.
setWorkflowRunParamDAO(WorkflowRunParamDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
setWorkflowRunParamDAO.
setWorkflowRunParamDAO(WorkflowRunParamDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
Setter for the field workflowRunParamDAO.
setWorkflowRunParamDAO(WorkflowRunParamDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
setWorkflowRunParamDAO.
setWorkflowRunParamId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
setWorkflowRunParamId.
setWorkflowRunParams(SortedSet<WorkflowRunParam>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
Setter for the field workflowRunParams.
setWorkflowRunProcessings(Collection<Processing>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
Setter for the field workflowRunProcessings.
setWorkflowRunRunning(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setWorkflowRunRunning.
setWorkflowRunRunningWithSample(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setWorkflowRunRunningWithSample.
setWorkflowRuns(Set<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.IUS
Setter for the field workflowRuns.
setWorkflowRuns(Set<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.Lane
Setter for the field workflowRuns.
setWorkflowRuns(SortedSet<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.Workflow
Setter for the field workflowRuns.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController
Setter for the field workflowRunService.
setWorkflowRunWithSample(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession
setWorkflowRunWithSample.
setWorkflows(ArrayList<WorkflowInfo>) - Method in class net.sourceforge.seqware.pipeline.bundle.BundleInfo
Setter for the field workflows.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.seqware.common.ContextImpl
Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController
Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails
Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController
Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController
Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController
Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController
Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController
Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController
Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController
Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController
Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController
Setter for the field workflowService.
setWorkflowSqwVersion(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
setWorkflowSqwVersion.
setWorkflowType(String) - Method in class net.sourceforge.seqware.common.model.Workflow
 
setWorkflowType(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
setXREFLINK(AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
Sets the value of the xreflink property.
setZygosity(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant
Setter for the field zygosity.
SGID - Class in com.github.seqware.queryengine.util
A wrapper for our eventual choice of globally unique primary key which may or may not be UUIDs.
SGID() - Constructor for class com.github.seqware.queryengine.util.SGID
Create a new SGID
SGID(String) - Constructor for class com.github.seqware.queryengine.util.SGID
Generate a SGID that can look up things given only a rowKey.
SGID(SGID) - Constructor for class com.github.seqware.queryengine.util.SGID
Clone a given SGID
SGID(long, long, long, String) - Constructor for class com.github.seqware.queryengine.util.SGID
Back-end constructor, create a fully functional SGID
SGID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
SGID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
SGID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
SGIDIO - Class in com.github.seqware.queryengine.impl.protobufIO
SGIDIO class.
SGIDIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.SGIDIO
 
SGIDIterable<T extends Atom> - Class in com.github.seqware.queryengine.util
A bit of a hack class, allows us to have getCount as well as iterable
SGIDIterable(Iterable<SGID>, Class<T>) - Constructor for class com.github.seqware.queryengine.util.SGIDIterable
Constructor for SGIDIterable.
SGIDIterable.SGIDIterator - Class in com.github.seqware.queryengine.util
 
SGIDIterable.SGIDIterator() - Constructor for class com.github.seqware.queryengine.util.SGIDIterable.SGIDIterator
 
SGIDTB - Class in com.github.seqware.queryengine.impl.tuplebinderIO
SGIDTB class.
SGIDTB() - Constructor for class com.github.seqware.queryengine.impl.tuplebinderIO.SGIDTB
 
ShareExperiment - Class in net.sourceforge.seqware.common.model
ShareExperiment generated by hbm2java
ShareExperiment() - Constructor for class net.sourceforge.seqware.common.model.ShareExperiment
Constructor for ShareExperiment.
ShareExperiment(int, Experiment, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareExperiment
Constructor for ShareExperiment.
ShareExperiment(int, Experiment, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareExperiment
Constructor for ShareExperiment.
ShareExperimentDAO - Interface in net.sourceforge.seqware.common.dao
ShareExperimentDAO interface.
ShareExperimentDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ShareExperimentDAOHibernate class.
ShareExperimentDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
 
ShareExperimentService - Interface in net.sourceforge.seqware.common.business
ShareExperimentService interface.
ShareExperimentServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ShareExperimentServiceImpl class.
ShareExperimentServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
 
ShareFile - Class in net.sourceforge.seqware.common.model
ShareFile generated by hbm2java
ShareFile() - Constructor for class net.sourceforge.seqware.common.model.ShareFile
Constructor for ShareFile.
ShareFile(int, File, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareFile
Constructor for ShareFile.
ShareFile(int, File, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareFile
Constructor for ShareFile.
ShareFileDAO - Interface in net.sourceforge.seqware.common.dao
ShareFileDAO interface.
ShareFileDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ShareFileDAOHibernate class.
ShareFileDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
 
ShareFileService - Interface in net.sourceforge.seqware.common.business
ShareFileService interface.
ShareFileServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ShareFileServiceImpl class.
ShareFileServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
 
ShareLane - Class in net.sourceforge.seqware.common.model
ShareLane generated by hbm2java
ShareLane() - Constructor for class net.sourceforge.seqware.common.model.ShareLane
Constructor for ShareLane.
ShareLane(int, Lane, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareLane
Constructor for ShareLane.
ShareLane(int, Lane, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareLane
Constructor for ShareLane.
ShareLaneDAO - Interface in net.sourceforge.seqware.common.dao
ShareLaneDAO interface.
ShareLaneDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ShareLaneDAOHibernate class.
ShareLaneDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
 
ShareLaneService - Interface in net.sourceforge.seqware.common.business
ShareLaneService interface.
ShareLaneServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ShareLaneServiceImpl class.
ShareLaneServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
 
ShareProcessing - Class in net.sourceforge.seqware.common.model
ShareProcessing generated by hbm2java
ShareProcessing() - Constructor for class net.sourceforge.seqware.common.model.ShareProcessing
Constructor for ShareProcessing.
ShareProcessing(int, Processing, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareProcessing
Constructor for ShareProcessing.
ShareProcessing(int, Processing, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareProcessing
Constructor for ShareProcessing.
ShareProcessingDAO - Interface in net.sourceforge.seqware.common.dao
ShareProcessingDAO interface.
ShareProcessingDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ShareProcessingDAOHibernate class.
ShareProcessingDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
 
ShareProcessingService - Interface in net.sourceforge.seqware.common.business
ShareProcessingService interface.
ShareProcessingServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ShareProcessingServiceImpl class.
ShareProcessingServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
 
ShareSample - Class in net.sourceforge.seqware.common.model
ShareSample generated by hbm2java
ShareSample() - Constructor for class net.sourceforge.seqware.common.model.ShareSample
Constructor for ShareSample.
ShareSample(int, Sample, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareSample
Constructor for ShareSample.
ShareSample(int, Sample, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareSample
Constructor for ShareSample.
ShareSampleDAO - Interface in net.sourceforge.seqware.common.dao
ShareSampleDAO interface.
ShareSampleDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ShareSampleDAOHibernate class.
ShareSampleDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
 
ShareSampleService - Interface in net.sourceforge.seqware.common.business
ShareSampleService interface.
ShareSampleServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ShareSampleServiceImpl class.
ShareSampleServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
 
ShareStudy - Class in net.sourceforge.seqware.common.model
ShareStudy class.
ShareStudy() - Constructor for class net.sourceforge.seqware.common.model.ShareStudy
Constructor for ShareStudy.
ShareStudyDAO - Interface in net.sourceforge.seqware.common.dao
ShareStudyDAO interface.
ShareStudyDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ShareStudyDAOHibernate class.
ShareStudyDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate
Constructor for ShareStudyDAOHibernate.
ShareStudyService - Interface in net.sourceforge.seqware.common.business
ShareStudyService interface.
ShareStudyServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ShareStudyServiceImpl class.
ShareStudyServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
Constructor for ShareStudyServiceImpl.
ShareValidatorController - Class in net.sourceforge.solexatools.webapp.controller
ShareValidatorController class.
ShareValidatorController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
Constructor for ShareValidatorController.
ShareWorkflowRun - Class in net.sourceforge.seqware.common.model
ShareWorkflowRun class.
ShareWorkflowRun() - Constructor for class net.sourceforge.seqware.common.model.ShareWorkflowRun
Constructor for ShareWorkflowRun.
ShareWorkflowRunDAO - Interface in net.sourceforge.seqware.common.dao
ShareWorkflowRunDAO interface.
ShareWorkflowRunDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
ShareWorkflowRunDAOHibernate class.
ShareWorkflowRunDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
Constructor for ShareWorkflowRunDAOHibernate.
ShareWorkflowRunService - Interface in net.sourceforge.seqware.common.business
ShareWorkflowRunService interface.
ShareWorkflowRunServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ShareWorkflowRunServiceImpl class.
ShareWorkflowRunServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
Constructor for ShareWorkflowRunServiceImpl.
SignUpController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
SignUpController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SignUpController
Constructor for SignUpController.
SimpleFileLock - Class in net.sourceforge.seqware.common.util.filetools.lock
Deprecated. 
SimpleFileLock(String) - Constructor for class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
Deprecated. Constructor for SimpleFileLock.
SimpleFileLock(File) - Constructor for class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock
Deprecated. Constructor for SimpleFileLock.
SimpleModelManager - Class in com.github.seqware.queryengine.impl
A Simple implementation of the CreateUpdateManager interface.
SimpleModelManager() - Constructor for class com.github.seqware.queryengine.impl.SimpleModelManager
 
SimpleModelManager.AtomStatePair - Class in com.github.seqware.queryengine.impl
 
SimpleModelManager.AtomStatePair(Atom, CreateUpdateManager.State) - Constructor for class com.github.seqware.queryengine.impl.SimpleModelManager.AtomStatePair
 
SimplePersistentBackEnd - Class in com.github.seqware.queryengine.impl
A toy backend implementation that writes all stores objects to disk using Java persistence.
SimplePersistentBackEnd(StorageInterface) - Constructor for class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
Constructor for SimplePersistentBackEnd.
single - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
 
size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
 
size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
 
size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
 
SIZE_COUNT_FILE - Static variable in class net.sourceforge.solexatools.util.PaginationUtil
Constant SIZE_COUNT_FILE=5
SIZE_COUNT_TREE - Static variable in class net.sourceforge.solexatools.util.PaginationUtil
Constant SIZE_COUNT_TREE=20
sleep(int) - Static method in class net.sourceforge.seqware.common.util.processtools.ProcessTools
sleep.
SNV - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant SNV=1
SOFeatureImporter - Class in com.github.seqware.queryengine.system.importers
Importer using a new interface to the parameters in order to support SO importing and the specification of a tag set and reference to attach to.
SOFeatureImporter() - Constructor for class com.github.seqware.queryengine.system.importers.SOFeatureImporter
 
someString() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibraryResource
someString.
SORT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant SORT_NAME="sortname"
SORT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
Constant SORT_NAME="sortname"
SORT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant SORT_NAME="sortname"
SORT_ORDER - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant SORT_ORDER="sortorder"
SORT_ORDER - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
Constant SORT_ORDER="sortorder"
SORT_ORDER - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant SORT_ORDER="sortorder"
SORT_ORDER_ASC - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant SORT_ORDER_ASC="asc"
SORT_ORDER_ASC - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant SORT_ORDER_ASC="asc"
SORT_ORDER_DESC - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant SORT_ORDER_DESC="desc"
SORT_ORDER_DESC - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant SORT_ORDER_DESC="desc"
source - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
source - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
 
source - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
 
source - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
 
SOURCE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
sourceSet - Variable in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner.PluginRunnerMapper
the feature set that we will be reading
spaceSeparateMy(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
 
splitFile(File, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
splitFile.
spotdecodemethod - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR
 
spotdecodespec - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR
 
spotdescriptor - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
 
SQLQUERYFAILED - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant SQLQUERYFAILED=82
SqwFile - Class in net.sourceforge.seqware.pipeline.workflowV2.model
a file object which has all information for provision
SqwFile() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
 
stackTraceToString(Throwable) - Static method in class net.sourceforge.seqware.common.util.exceptiontools.ExceptionTools
stackTraceToString.
START_ALL_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
Constant START_ALL_QUERYDATELONG="start-ALL_query-date-long"
START_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
START_PMC_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
Constant START_PMC_QUERYDATELONG="start-PMC_query-date-long"
START_PMCSI_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
Constant START_PMCSI_QUERYDATELONG="start-PMCSI_query-date-long"
START_QUAL_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
Constant START_QUAL_QUERYDATELONG="start-QUAL_query-date-long"
startCommand(Map<String, String>, String) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
startCommand.
startCommand(String) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
startCommand.
startCommand(String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
startCommand.
startCommand(Map<String, String>, String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
An alternate runner that launches a process and returns it so that the caller can process it's output directly.
STARTCOUNTDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
Constant STARTCOUNTDATELONG="start-count-date-long"
STARTDUMP_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler
Constant STARTDUMP_QUERYDATELONG="start-dump_query-date-long"
startPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
 
startPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
startService(String[]) - Static method in class com.github.seqware.queryengine.system.rest.QueryEngineService
 
startTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
startTransaction.
startTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
startTransaction.
startTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
startTransaction.
startTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store
startTransaction.
startTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface
startTransaction.
status - Variable in exception net.sourceforge.seqware.common.util.ExitException
 
statusCounts - Variable in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
 
stderr - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
stderr(String) - Static method in class net.sourceforge.seqware.common.util.Log
stderr.
StdErr - Class in net.sourceforge.seqware.common.util.processtools.stderr
StdErr class.
StdErr() - Constructor for class net.sourceforge.seqware.common.util.processtools.stderr.StdErr
 
stderr2string(Process) - Static method in class net.sourceforge.seqware.common.util.processtools.stderr.StdErr
stderr2string.
StderrRedirect - Annotation Type in net.sourceforge.seqware.pipeline.module
Annotation type to tag where to start Stderr redirect Created by IntelliJ IDEA.
stdout - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
stdout(String) - Static method in class net.sourceforge.seqware.common.util.Log
stdout.
StdOut - Class in net.sourceforge.seqware.common.util.processtools.stdout
StdOut class.
StdOut() - Constructor for class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
 
stdout2file(Process, File, boolean) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
stdout2file.
stdout2file(Process, ArrayList<File>, boolean, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
stdout2file.
stdout2fileBinary(Process, File) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
stdout2fileBinary.
stdout2fileBinary(Process, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
stdout2fileBinary.
stdout2fileEncoded(Process, File) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
stdout2fileEncoded.
stdout2fileEncoded(Process, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
stdout2fileEncoded.
stdout2fileEncodedStripQualPrimer(Process, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
stdout2fileEncodedStripQualPrimer.
STDOUTERR - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant STDOUTERR=90
StdoutRedirect - Annotation Type in net.sourceforge.seqware.pipeline.module
Interface for declaring when to do the Created by IntelliJ IDEA.
stop() - Static method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceMain
stop.
STOP_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
stopPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
 
stopPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
storage - Variable in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
 
StorageInterface - Class in com.github.seqware.queryengine.backInterfaces
Defines a very basic interface that allows us to abstract whether we write to files or to databases or just keep things in memory
StorageInterface() - Constructor for class com.github.seqware.queryengine.backInterfaces.StorageInterface
 
store(Atom...) - Method in interface com.github.seqware.queryengine.backInterfaces.LowLevelBackEndInterface
Store obj in the back-end.
store(Atom...) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
Store obj in the back-end.
Store - Class in net.sourceforge.seqware.queryengine.backend.store
Abstract Store class.
Store() - Constructor for class net.sourceforge.seqware.queryengine.backend.store.Store
 
StoreInterface - Interface in net.sourceforge.seqware.queryengine.backend.store
StoreInterface interface.
strand - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
strand - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
STRAND_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
STRING - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant STRING=24
STRING - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant STRING=24
STRINGID - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model
Constant STRINGID=20
StringId - Class in net.sourceforge.seqware.queryengine.backend.model
StringId class.
StringId() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.StringId
 
StringIdTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders
StringIdTB class.
StringIdTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.StringIdTB
 
StringUtils - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus
StringUtils class.
StringUtils() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.StringUtils
 
Study - Class in net.sourceforge.seqware.common.model
 
Study() - Constructor for class net.sourceforge.seqware.common.model.Study
Constructor for Study.
study - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudySet
 
STUDY_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant STUDY_ATTRIBUTES="Header.STUDY_ATTRIBUTES.getTitle()"
STUDY_ID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
Constant STUDY_ID="study_id"
STUDY_ID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant STUDY_ID="study_id"
STUDY_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
Constant STUDY_PREFIX="study_"
STUDY_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant STUDY_SWA="Header.STUDY_SWA.getTitle()"
STUDY_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant STUDY_TAG_PREFIX="Header.STUDY_TAG_PREFIX.getTitle()"
STUDY_TITLE - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant STUDY_TITLE="Header.STUDY_TITLE.getTitle()"
STUDY_VIEW - Static variable in class net.sourceforge.solexatools.util.Constant
Constant STUDY_VIEW="redirect:/myStudyList.htm"
studyabstract - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
 
StudyAttribute - Class in net.sourceforge.seqware.common.model
StudyAttribute generated by hbm2java
StudyAttribute() - Constructor for class net.sourceforge.seqware.common.model.StudyAttribute
Constructor for StudyAttribute.
StudyAttribute(int, Study, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyAttribute
Constructor for StudyAttribute.
StudyAttribute(int, Study, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyAttribute
Constructor for StudyAttribute.
studyattribute - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES
 
StudyAttributeDAO - Interface in net.sourceforge.seqware.common.dao
StudyAttributeDAO interface.
StudyAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
StudyAttributeDAOHibernate class.
StudyAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate
 
studyattributes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
 
StudyBuildTree - Class in net.sourceforge.solexatools.util
StudyBuildTree class.
StudyBuildTree() - Constructor for class net.sourceforge.solexatools.util.StudyBuildTree
 
StudyController - Class in net.sourceforge.solexatools.webapp.controller
StudyController
StudyController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyController
Constructor for StudyController.
StudyController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyController
Constructor for StudyController.
StudyDAO - Interface in net.sourceforge.seqware.common.dao
StudyDAO interface.
StudyDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
StudyDAOHibernate class.
StudyDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
Constructor for StudyDAOHibernate.
studydescription - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
 
StudyHtmlUtil - Class in net.sourceforge.solexatools.util
StudyHtmlUtil class.
StudyHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.StudyHtmlUtil
 
StudyIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries
StudyIdFilesResource class.
StudyIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesResource
Constructor for StudyIdFilesResource.
StudyIdFilesTSVResource - Class in net.sourceforge.seqware.webservice.resources.queries
StudyIdFilesTSVResource class.
StudyIdFilesTSVResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesTSVResource
Constructor for StudyIdFilesTSVResource.
StudyIDFilter - Class in net.sourceforge.seqware.webservice.resources.filters
StudyIDFilter class.
StudyIDFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.StudyIDFilter
 
StudyIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
StudyIDResource class.
StudyIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.StudyIDResource
Constructor for StudyIDResource.
StudyLink - Class in net.sourceforge.seqware.common.model
StudyLink generated by hbm2java
StudyLink() - Constructor for class net.sourceforge.seqware.common.model.StudyLink
Constructor for StudyLink.
StudyLink(int, Study, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyLink
Constructor for StudyLink.
StudyLink(int, Study, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyLink
Constructor for StudyLink.
studylink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS
 
StudyLinkDAO - Interface in net.sourceforge.seqware.common.dao
StudyLinkDAO interface.
StudyLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
StudyLinkDAOHibernate class.
StudyLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate
 
studylinks - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
 
StudyList - Class in net.sourceforge.seqware.common.model.lists
StudyList class.
StudyList() - Constructor for class net.sourceforge.seqware.common.model.lists.StudyList
Constructor for StudyList.
StudyListController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
StudyListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyListController
Constructor for StudyListController.
StudyListDetailsController - Class in net.sourceforge.solexatools.webapp.controller
StudyListDetailsController class.
StudyListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
Constructor for StudyListDetailsController.
StudyListDetailsFlatController - Class in net.sourceforge.solexatools.webapp.controller
 
StudyListDetailsFlatController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
 
studyref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
 
studyref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
StudyReportBoxController - Class in net.sourceforge.solexatools.webapp.controller
StudyReportBoxController class.
StudyReportBoxController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
 
StudyReportController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
StudyReportController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportController
Constructor for StudyReportController.
StudyReportSetupController - Class in net.sourceforge.solexatools.webapp.controller
StudyReportSetupController class.
StudyReportSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportSetupController
 
StudyReportTableController - Class in net.sourceforge.solexatools.webapp.controller
StudyReportTableController class.
StudyReportTableController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constructor for StudyReportTableController.
StudyResource - Class in net.sourceforge.seqware.webservice.resources.tables
StudyResource class.
StudyResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.StudyResource
Constructor for StudyResource.
StudySampleReportFileLineItem - Class in net.sourceforge.solexatools.webapp.metamodel
StudySampleReportFileLineItem class.
StudySampleReportFileLineItem(Sample, Sample, IUS, File) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
Constructor for StudySampleReportFileLineItem.
StudySampleReportLineItem - Class in net.sourceforge.solexatools.webapp.metamodel
StudySampleReportLineItem class.
StudySampleReportLineItem(Sample, Sample, String[]) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
Constructor for StudySampleReportLineItem.
StudyService - Interface in net.sourceforge.seqware.common.business
StudyService interface.
StudyServiceImpl - Class in net.sourceforge.seqware.common.business.impl
StudyServiceImpl class.
StudyServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
Constructor for StudyServiceImpl.
StudySet - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
StudySet() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudySet
 
StudySetupController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController
StudySetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudySetupController
Constructor for StudySetupController.
studytitle - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
 
StudyType - Class in net.sourceforge.seqware.common.model
StudyType class.
StudyType() - Constructor for class net.sourceforge.seqware.common.model.StudyType
 
StudyType - Class in net.sourceforge.seqware.queryengine.webservice.model
A Study is a container for a sequencing investigation that may comprise multiple experiments.
StudyType() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType
 
studytype - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
 
StudyType.DESCRIPTOR - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
StudyType.DESCRIPTOR() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
 
StudyType.DESCRIPTOR.STUDYTYPE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
StudyType.DESCRIPTOR.STUDYTYPE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE
 
StudyType.STUDYATTRIBUTES - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
StudyType.STUDYATTRIBUTES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES
 
StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
 
StudyType.STUDYLINKS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
StudyType.STUDYLINKS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS
 
StudyType.STUDYLINKS.STUDYLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
StudyType.STUDYLINKS.STUDYLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK
 
StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
 
StudyType.STUDYLINKS.STUDYLINK.URLLINK - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
StudyType.STUDYLINKS.STUDYLINK.URLLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK
 
StudyTypeDAO - Interface in net.sourceforge.seqware.common.dao
StudyTypeDAO interface.
StudyTypeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
StudyTypeDAOHibernate class.
StudyTypeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate
Constructor for StudyTypeDAOHibernate.
StudyTypeList - Class in net.sourceforge.seqware.common.model.lists
StudyTypeList class.
StudyTypeList() - Constructor for class net.sourceforge.seqware.common.model.lists.StudyTypeList
Constructor for StudyTypeList.
StudyTypeResource - Class in net.sourceforge.seqware.webservice.resources.tables
ExperimentResource class.
StudyTypeResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.StudyTypeResource
Constructor for ExperimentResource.
StudyTypeService - Interface in net.sourceforge.seqware.common.business
StudyTypeService interface.
StudyTypeServiceImpl - Class in net.sourceforge.seqware.common.business.impl
StudyTypeServiceImpl class.
StudyTypeServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
Constructor for StudyTypeServiceImpl.
StudyUpdateValidator - Class in net.sourceforge.solexatools.validation
 
StudyUpdateValidator() - Constructor for class net.sourceforge.solexatools.validation.StudyUpdateValidator
 
StudyValidator - Class in net.sourceforge.solexatools.validation
StudyValidator class.
StudyValidator() - Constructor for class net.sourceforge.solexatools.validation.StudyValidator
Constructor for StudyValidator.
subList(int, int, List) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
subList.
subList(HttpServletRequest, String, List<T>) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
subList.
subList(HttpServletRequest, String, int, List<T>) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
subList.
subListSD(HttpServletRequest, String, List) - Static method in class net.sourceforge.solexatools.util.PaginationUtil
subListSD.
submission - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionSet
 
submissionComment - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
submissionDate - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
submissionId - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
SubmissionSet - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionSet() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionSet
 
SubmissionType - Class in net.sourceforge.seqware.queryengine.webservice.model
A Submission type is used to describe an object that contains submission information, contacts for the submission, actions to be performed by the Archive, and file manifest.
SubmissionType() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
SubmissionType.ACTIONS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.ACTIONS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS
 
SubmissionType.ACTIONS.ACTION - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
 
SubmissionType.ACTIONS.ACTION.ADD - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION.ADD() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
 
SubmissionType.ACTIONS.ACTION.HOLD - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION.HOLD() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
 
SubmissionType.ACTIONS.ACTION.MODIFY - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION.MODIFY() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
 
SubmissionType.ACTIONS.ACTION.RELEASE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION.RELEASE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE
 
SubmissionType.ACTIONS.ACTION.SUPPRESS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION.SUPPRESS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS
 
SubmissionType.ACTIONS.ACTION.VALIDATE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION.VALIDATE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
 
SubmissionType.CONTACTS - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.CONTACTS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS
 
SubmissionType.CONTACTS.CONTACT - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.CONTACTS.CONTACT() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
 
SubmissionType.FILES - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.FILES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES
 
SubmissionType.FILES.FILE - Class in net.sourceforge.seqware.queryengine.webservice.model
Java class for anonymous complex type.
SubmissionType.FILES.FILE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
 
SUBMITTED - Static variable in class net.sourceforge.seqware.common.metadata.Metadata
Constant SUBMITTED="submitted"
SUCCESS - Static variable in class net.sourceforge.seqware.common.metadata.Metadata
Constant SUCCESS="success"
SUCCESS - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant SUCCESS=0
SUCCESS - Static variable in class net.sourceforge.seqware.pipeline.decider.Decider
Constant SUCCESS="success"
SUCCESS - Static variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
Constant SUCCESS="success"
sum - Variable in class net.sourceforge.seqware.queryengine.backend.model.Coverage
 
SummaryData - Class in net.sourceforge.solexatools.util
SummaryData class.
SummaryData() - Constructor for class net.sourceforge.solexatools.util.SummaryData
Constructor for SummaryData.
SummaryLaunchWorkflowController - Class in net.sourceforge.solexatools.webapp.controller
SummaryLaunchWorkflowController class.
SummaryLaunchWorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
Constructor for SummaryLaunchWorkflowController.
SummaryLaunchWorkflowController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController
Constructor for SummaryLaunchWorkflowController.
SummaryLine - Class in net.sourceforge.solexatools.util
SummaryLine class.
SummaryLine() - Constructor for class net.sourceforge.solexatools.util.SummaryLine
Constructor for SummaryLine.
supports(Class) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
supports(Class) - Method in class net.sourceforge.solexatools.validation.LaneValidator
supports(Class) - Method in class net.sourceforge.solexatools.validation.LoginValidator
Returns true if this Validator supports the specified Class, and false otherwise.
supports(Class) - Method in class net.sourceforge.solexatools.validation.SampleValidator
supports(Class) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
supports(Class) - Method in class net.sourceforge.solexatools.validation.SequencerRunWizardValidator
supports(Class) - Method in class net.sourceforge.solexatools.validation.StudyValidator
supports(Class) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
supports(Class) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
supports(Class) - Method in class net.sourceforge.solexatools.validation.WorkflowParamValidator
supports(Class) - Method in class net.sourceforge.solexatools.validation.WorkflowValidator
suppress - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
 
SV - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant SV=4
SV_COMPLEX - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant SV_COMPLEX=1
SV_DELETION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant SV_DELETION=2
SV_DELETION_AND_INVERSION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant SV_DELETION_AND_INVERSION=3
SV_DISPERSED_DUPLICATION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant SV_DISPERSED_DUPLICATION=4
SV_DUPLICATION_AND_INVERSION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant SV_DUPLICATION_AND_INVERSION=5
SV_INVERSION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant SV_INVERSION=6
SV_LOCATION_DOWNSTREAM - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant SV_LOCATION_DOWNSTREAM=2
SV_LOCATION_UNKNOWN - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant SV_LOCATION_UNKNOWN=0
SV_LOCATION_UPSTREAM - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant SV_LOCATION_UPSTREAM=1
SV_TANDEM_DUPLICATION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant SV_TANDEM_DUPLICATION=7
SV_UNKNOWN - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant SV_UNKNOWN=0
svType - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
sw - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
SwBadFileException - Exception in net.sourceforge.seqware.common.err
Created by IntelliJ IDEA.
SwBadFileException() - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException
Constructor for SwBadFileException.
SwBadFileException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException
Constructor for SwBadFileException.
SwBadFileException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException
Constructor for SwBadFileException.
SwBadFileException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException
Constructor for SwBadFileException.
SwBadModuleException - Exception in net.sourceforge.seqware.common.err
User: Xiaoshu Wang (xiao@renci.org) Date: 9/1/11 Time: 2:56 PM
SwBadModuleException() - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException
Constructor for SwBadModuleException.
SwBadModuleException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException
Constructor for SwBadModuleException.
SwBadModuleException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException
Constructor for SwBadModuleException.
SwBadModuleException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException
Constructor for SwBadModuleException.
SwParameterException - Exception in net.sourceforge.seqware.common.err
Created by IntelliJ IDEA.
SwParameterException() - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException
Constructor for SwParameterException.
SwParameterException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException
Constructor for SwParameterException.
SwParameterException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException
Constructor for SwParameterException.
SwParameterException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException
Constructor for SwParameterException.
SWQEFactory - Class in com.github.seqware.queryengine.factory
This is the SeqWare Query Engine factory and should be used as the primary entry-point for developers.
SWQEFactory() - Constructor for class com.github.seqware.queryengine.factory.SWQEFactory
 
SWQEFactory.Model_Type - Enum in com.github.seqware.queryengine.factory
' These types describe different types of our model objects, for example the in memory objects load everything into memory.
SWQEFactory.Serialization_Type - Enum in com.github.seqware.queryengine.factory
These describe different types of serialization only
SWQEFactory.Storage_Type - Enum in com.github.seqware.queryengine.factory
These describe different types of our back-end, whether we store to files, to a database, or simply keep things in memory
SwRunnerParameterException - Exception in net.sourceforge.seqware.common.err
User: Xiaoshu Wang (xiao@renci.org) Date: 9/6/11 Time: 3:20 PM
SwRunnerParameterException() - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException
Constructor for SwRunnerParameterException.
SwRunnerParameterException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException
Constructor for SwRunnerParameterException.
SwRunnerParameterException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException
Constructor for SwRunnerParameterException.
SwRunnerParameterException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException
Constructor for SwRunnerParameterException.
SymLinkFileReporter - Class in net.sourceforge.seqware.pipeline.plugins
SymLinkFileReporter class.
SymLinkFileReporter() - Constructor for class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter
Constructor for SymLinkFileReporter.

T

T__26 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant T__26=26
T__26 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant T__26=26
TabExpansionUtil - Class in net.sourceforge.seqware.common.util
A series of utility methods that produce human friendly output from tabbed output.
TabExpansionUtil() - Constructor for class net.sourceforge.seqware.common.util.TabExpansionUtil
 
table - Variable in class net.sourceforge.seqware.webservice.resources.tables.DatabaseResource
 
TABLE_MODEL - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant TABLE_MODEL="tablemodel"
TABLE_MODEL - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant TABLE_MODEL="tablemodel"
TABLE_SEL - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
Constant TABLE_SEL="tablesel"
TABLE_SEL - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
Constant TABLE_SEL="tablesel"
Tag - Class in com.github.seqware.queryengine.model
A Tag an instance of a TagSpec which contains all three of the values necessary for a GVF (ex: ID=ID_1 or Variant_seq=A,G or Reference_seq=G ).
TAG - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model
Constant TAG=10
Tag - Class in net.sourceforge.seqware.queryengine.backend.model
Tag class.
Tag() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.Tag
 
tag - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
 
tag - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
 
tag - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
 
tag - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
 
tag - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
 
Tag.Builder - Class in com.github.seqware.queryengine.model
 
Tag.Builder() - Constructor for class com.github.seqware.queryengine.model.Tag.Builder
 
Tag.ValueType - Enum in com.github.seqware.queryengine.model
 
TAG_CHAR - Static variable in class com.github.seqware.queryengine.system.importers.OBOImporter
Constant TAG_CHAR='n'
TagAnnotationByPositionImporter - Class in net.sourceforge.seqware.queryengine.tools.importers
TagAnnotationByPositionImporter class.
TagAnnotationByPositionImporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.TagAnnotationByPositionImporter
 
TagAnnotationImporter - Class in net.sourceforge.seqware.queryengine.tools.importers
TagAnnotationImporter class.
TagAnnotationImporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.TagAnnotationImporter
 
TagComparator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators
TagComparator class.
TagComparator() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators.TagComparator
 
TagDumper - Class in net.sourceforge.seqware.queryengine.tools.exporters
TagDumper class.
TagDumper() - Constructor for class net.sourceforge.seqware.queryengine.tools.exporters.TagDumper
 
tagElement(String, String, String, String, String) - Method in class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
Associate a tag with a particular element
Taggable<T> - Interface in com.github.seqware.queryengine.model.interfaces
Interface for all classes that can be tagged.
Taggable.NestedLevel - Class in com.github.seqware.queryengine.model.interfaces
This class represents both the tags that may be present at a particular level of the nested hash structure as well as tags that may be further up
Taggable.NestedLevel() - Constructor for class com.github.seqware.queryengine.model.interfaces.Taggable.NestedLevel
 
taggedRequest(String, String) - Method in class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
Retrieve resources tagged with a particular key on a particular element.
tagIndexTable - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
 
TagIO - Class in com.github.seqware.queryengine.impl.protobufIO
TagIO class.
TagIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.TagIO
 
TagKeyCreator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators
TagKeyCreator class.
TagKeyCreator(TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.TagKeyCreator
Constructor for TagKeyCreator.
TagKeyOnlyCreator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators
TagKeyOnlyCreator class.
TagKeyOnlyCreator(TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.TagKeyOnlyCreator
Constructor for TagKeyOnlyCreator.
TagListingResource - Class in com.github.seqware.queryengine.system.rest.resources
 
TagListingResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.TagListingResource
 
TagResource - Class in com.github.seqware.queryengine.system.rest.resources
Tag resource.
TagResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.TagResource
 
TagResource - Class in net.sourceforge.seqware.queryengine.webservice.view
TagResource class.
TagResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.TagResource
 
tags - Variable in class net.sourceforge.seqware.queryengine.backend.model.Model
 
tags - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
TAGS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
TAGS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
TagSet - Interface in com.github.seqware.queryengine.model
A set of Tag specifications
TagSet.Builder - Class in com.github.seqware.queryengine.model
 
TagSet.Builder() - Constructor for class com.github.seqware.queryengine.model.TagSet.Builder
 
TAGSET_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
TagSetCreator - Class in com.github.seqware.queryengine.system
Quick and dirty TagSet creator.
TagSetCreator() - Constructor for class com.github.seqware.queryengine.system.TagSetCreator
Constructor for TagSetCreator.
tagSetIDs - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
TagSetIO - Class in com.github.seqware.queryengine.impl.protobufIO
TagSetIO class.
TagSetIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.TagSetIO
 
TagSetListingResource - Class in com.github.seqware.queryengine.system.rest.resources
 
TagSetListingResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.TagSetListingResource
 
TagSetResource - Class in com.github.seqware.queryengine.system.rest.resources
TagSet resource.
TagSetResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.TagSetResource
 
TAGSETS_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
Constant TAGSETS_PARAM='s'
tagsOfElementRequest(String) - Method in class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
Retrieve resources and list their tags.
TAGSPECIDS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
TagSpecIO - Class in com.github.seqware.queryengine.impl.protobufIO
TagSpecIO class.
TagSpecIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.TagSpecIO
 
TagTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders
TagTB class.
TagTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.TagTB
 
TagUtils - Class in net.sourceforge.solexatools.util
TagUtils class.
TagUtils() - Constructor for class net.sourceforge.solexatools.util.TagUtils
 
target - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
 
target - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
 
target - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE
 
target - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS
 
taxonid - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
 
temp - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
templateFile - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
TemplateResource - Class in net.sourceforge.seqware.queryengine.webservice.view
TemplateResource class.
TemplateResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.TemplateResource
 
test() - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
 
test() - Method in interface com.github.seqware.queryengine.plugins.PluginInterface
test.
test(String[]) - Method in class net.sourceforge.seqware.pipeline.tools.ReportTest
test.
TEST_TABLE_PREFIX - Static variable in class com.github.seqware.queryengine.impl.HBaseStorage
Constant TEST_TABLE_PREFIX="Constants.Term.NAMESPACE.getTermValue(S"{trunked}
testBundle(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
testBundle.
testBundle(File, File, String, String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
A bundle test occurs without metadata writeback
TestDatabaseCreator - Class in net.sourceforge.seqware.metadb.util
TestDatabaseCreator class.
TestDatabaseCreator() - Constructor for class net.sourceforge.seqware.metadb.util.TestDatabaseCreator
 
testIfNull(Object) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
testIfNull.
testIfNull(Object) - Method in class net.sourceforge.seqware.webservice.resources.BasicResource
testIfNull.
testIfNull(Object) - Method in class net.sourceforge.seqware.webservice.resources.BasicRestlet
testIfNull.
TestModule - Class in net.sourceforge.seqware.pipeline.module
This is an empty module mainly for testing purpose.
TestModule() - Constructor for class net.sourceforge.seqware.pipeline.module.TestModule
 
TextDumper - Class in net.sourceforge.seqware.queryengine.tools.exporters
TextDumper class.
TextDumper() - Constructor for class net.sourceforge.seqware.queryengine.tools.exporters.TextDumper
 
thickEnd - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
thickStart - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
three_param_predicate() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
three_param_predicate.
TIMESTAMP_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
title - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
 
title - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
 
title - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.ExperimentList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.FileList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.IUSList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.LaneList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.LibrarySelectionList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.LibrarySourceList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.LibraryStrategyList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.OrganismList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.PlatformList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.ProcessingList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.ReturnValueList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.SampleList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.SequencerRunList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.StudyList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.StudyTypeList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowParamList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowRunList
 
tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2
 
TmpFileStorage - Class in com.github.seqware.queryengine.impl
Stores objects in the temporary directory of the disk
TmpFileStorage(SerializationInterface) - Constructor for class com.github.seqware.queryengine.impl.TmpFileStorage
Constructor for TmpFileStorage.
toBaseN(int, int) - Static method in class com.github.seqware.queryengine.kernel.Compression
Converts an integer into a string representation of certain base.
toBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
toBuilder() - Method in class com.github.seqware.queryengine.model.Feature
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.FeatureSet
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in interface com.github.seqware.queryengine.model.Group
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.FeatureList
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.hbasemrlazy.MRLazyFeatureSet
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryPlugin
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.interfaces.ACL
Create an ACL builder started with a copy of this
toBuilder() - Method in interface com.github.seqware.queryengine.model.interfaces.Buildable
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in interface com.github.seqware.queryengine.model.Plugin
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.PluginRun
 
toBuilder() - Method in interface com.github.seqware.queryengine.model.Reference
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in interface com.github.seqware.queryengine.model.ReferenceSet
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.Tag
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in interface com.github.seqware.queryengine.model.TagSet
Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.User
Creates a new builder initialized with the fields of an existing object
tokenNames - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant tokenNames="new String[] {, , ,"{trunked}
TOMBSTONE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
toString() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager.AtomStatePair
 
toString() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
toString() - Method in class com.github.seqware.queryengine.util.FSGID
toString() - Method in class com.github.seqware.queryengine.util.SGID
toString() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
 
toString() - Method in class net.sourceforge.seqware.common.model.Expense
toString() - Method in class net.sourceforge.seqware.common.model.Experiment
toString() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
toString.
toString() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
toString.
toString() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
toString() - Method in class net.sourceforge.seqware.common.model.File
toString() - Method in class net.sourceforge.seqware.common.model.FileType
toString() - Method in class net.sourceforge.seqware.common.model.Invoice
toString() - Method in class net.sourceforge.seqware.common.model.IUS
toString() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
toString() - Method in class net.sourceforge.seqware.common.model.Lane
toString() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
toString() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
 
toString() - Method in class net.sourceforge.seqware.common.model.LibrarySource
 
toString() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
 
toString() - Method in class net.sourceforge.seqware.common.model.Organism
 
toString() - Method in class net.sourceforge.seqware.common.model.Platform
 
toString() - Method in class net.sourceforge.seqware.common.model.Processing
toString() - Method in class net.sourceforge.seqware.common.model.Project
toString() - Method in class net.sourceforge.seqware.common.model.Registration
toString() - Method in class net.sourceforge.seqware.common.model.Sample
toString() - Method in class net.sourceforge.seqware.common.model.SequencerRun
toString() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
toString() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
toString() - Method in class net.sourceforge.seqware.common.model.ShareStudy
toString() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
toString() - Method in class net.sourceforge.seqware.common.model.Study
toString() - Method in class net.sourceforge.seqware.common.model.StudyType
toString() - Method in class net.sourceforge.seqware.common.model.Workflow
toString() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
toString() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
toString() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
toString() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
toString.
toString() - Method in class net.sourceforge.seqware.common.module.FileMetadata
 
toString() - Method in class net.sourceforge.seqware.common.module.ReturnValue
toString() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.RunInfo
 
toString() - Method in class net.sourceforge.seqware.pipeline.plugins.BatchMetadataInjection.SampleInfo
 
toString() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
 
toString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
toString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
 
toString(WorkflowRunReportRow, StringBuilder) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource
toString.
totalDataBlocks - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
 
totalReads - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
 
totalSpots - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
 
totalSteps - Variable in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
 
totalSteps - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
trace(Object) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.debug(Object).
trace(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.debug(Object,Throwable).
transcriptassembly - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
 
transcriptId - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
 
transcriptsequencing - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
 
translatedSequence - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
 
TRANSLOCATION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant TRANSLOCATION=5
TRANSLOCATION_COMPLEX - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant TRANSLOCATION_COMPLEX=3
TRANSLOCATION_INTERCHR - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant TRANSLOCATION_INTERCHR=2
TRANSLOCATION_INTRACHR - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant TRANSLOCATION_INTRACHR=1
TRANSLOCATION_UNKNOWN - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant TRANSLOCATION_UNKNOWN=0
translocationDestinationContig - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
translocationDestinationStartPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
translocationDestinationStopPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
translocationType - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
TreeNodeHtmlUtil - Class in net.sourceforge.solexatools.util
TreeNodeHtmlUtil class.
TreeNodeHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
 
TTLable - Interface in com.github.seqware.queryengine.model.interfaces
Interface for object that can be set to expire at some point in the future.
two_param_predicate() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
two_param_predicate.
type - Variable in class com.github.seqware.queryengine.util.LazyReference
 
type - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 
TYPE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
TYPE_TREE - Static variable in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
Constant TYPE_TREE="sr"
TYPE_TREE - Static variable in class net.sourceforge.solexatools.util.StudyHtmlUtil
Constant TYPE_TREE="st"
TYPE_TREE_COMPLETED - Static variable in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
Constant TYPE_TREE_COMPLETED="wfr"
TYPE_TREE_RUNNNING - Static variable in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
Constant TYPE_TREE_RUNNNING="wfrr"

U

U87LargeDeletionVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
U87LargeDeletionVariantImportWorker class.
U87LargeDeletionVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.U87LargeDeletionVariantImportWorker
Constructor for U87LargeDeletionVariantImportWorker.
U87TranslocationVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
U87TranslocationVariantImportWorker class.
U87TranslocationVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.U87TranslocationVariantImportWorker
Constructor for U87TranslocationVariantImportWorker.
unBindSessionFromTheThread() - Static method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions
unBindSessionFromTheThread.
UNCKerberos - Class in net.sourceforge.solexatools.authentication
UNCKerberos class.
UNCKerberos() - Constructor for class net.sourceforge.solexatools.authentication.UNCKerberos
 
UNCKerberos.NamePasswordCallbackHandler - Class in net.sourceforge.solexatools.authentication
 
UNCKerberos.NamePasswordCallbackHandler(String, String) - Constructor for class net.sourceforge.solexatools.authentication.UNCKerberos.NamePasswordCallbackHandler
 
Unclassified - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode
Constant Unclassified=1
units - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
 
units - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
 
units - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
 
units - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
 
units - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
 
UNKNOWN - Static variable in class net.sourceforge.seqware.common.metadata.Metadata
Constant UNKNOWN="unknown"
UNKNOWN - Static variable in class net.sourceforge.seqware.common.module.ReturnValue
Constant UNKNOWN=130
UNKNOWN_TYPE - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant UNKNOWN_TYPE=0
UNKNOWN_VALUE - Static variable in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
UNKNOWN_ZYGOSITY - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Constant UNKNOWN_ZYGOSITY=0
unmarshal(FileList) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeFileSet
unmarshal(IUSList) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeIUSSortedSet
unmarshal(LaneList) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeLaneSortedSet
unmarshal(String) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeXML
unMarshal(T, Reader) - Method in class net.sourceforge.seqware.common.util.xmltools.JaxbObject
Turn an XML stream into an object, if possible.
unMarshal(Document, T) - Method in class net.sourceforge.seqware.common.util.xmltools.JaxbObject
Turn an XML stream into an object, if possible.
unMarshal(JaxbObject, Object, String) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools
unMarshal.
unpackageBundle(File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
unpackageBundle.
unpackageBundleFromS3(String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
unpackageBundleFromS3.
unpackArchive(File, File, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.ZipFileUtil
Unpack a zip file
UnZip - Class in net.sourceforge.seqware.pipeline.tools
UnZip class.
UnZip() - Constructor for class net.sourceforge.seqware.pipeline.tools.UnZip
 
unzipFile(File, File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
FIXME: should make this optional to keep the original file
unzipFileOld(File, File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
FIXME: should make this optional to keep the original file
unzipPkg(String) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner
FIXME: this needs to be migrated to something that is ZIP64 aware.
update(Atom...) - Method in interface com.github.seqware.queryengine.backInterfaces.LowLevelBackEndInterface
Crawl through obj and update changes in the back-end.
update(Atom...) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
Crawl through obj and update changes in the back-end.
update(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
update.
update(Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
update.
update(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
update.
update(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
update.
update(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService
update.
update(Integer, FileAttribute) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService
update.
update(Registration, File) - Method in interface net.sourceforge.seqware.common.business.FileService
update.
update(File) - Method in interface net.sourceforge.seqware.common.business.FileService
update.
update(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl
update.
update(Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
update.
update(Registration, Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
update.
update(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl
update.
update(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl
update.
update(Integer, FileAttribute) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl
update.
update(File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
update.
update(Registration, File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
update.
update(Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
update.
update(Registration, Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
update.
update(IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
update.
update(Registration, IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
update.
update(Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
update.
update(Registration, Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
update.
update(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
update.
update(ProcessingIus) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
update.
update(ProcessingLanes) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
update.
update(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
update.
update(ProcessingSamples) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
update.
update(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
update.
update(Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
update.
update(Registration, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
update.
update(ProcessingStudies) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
update.
update(Project) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
update.
update(RegistrationDTO) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
update.
update(Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
update.
update(Registration, Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
update.
update(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
update.
update(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
update.
update(ShareExperiment) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
update.
update(ShareFile) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
update.
update(ShareLane) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
update.
update(ShareProcessing) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
update.
update(ShareSample) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
update.
update(ShareStudy) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
update.
update(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
update.
update(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
update.
update(Registration, Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
update.
update(StudyType) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
update.
update(WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
update.
update(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
update.
update(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
update.
update(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
update.
update(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
update.
update(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
update.
update(WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
update.
update(WorkflowRun, List<Integer>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
update.
update(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
update.
update(Registration, WorkflowRun, List<Integer>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
update.
update(Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
update.
update(Registration, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
update.
update(Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
update.
update(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
update.
update(IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService
update.
update(Registration, IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService
update.
update(Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService
update.
update(Registration, Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService
update.
update(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService
update.
update(ProcessingIus) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService
update.
update(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService
update.
update(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService
update.
update(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService
update.
update(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService
update.
update(Registration, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
update.
update(Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
update.
update(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService
update.
update(Project) - Method in interface net.sourceforge.seqware.common.business.ProjectService
update.
update(RegistrationDTO) - Method in interface net.sourceforge.seqware.common.business.RegistrationService
update.
update(Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService
update.
update(Registration, Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService
update.
update(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
update.
update(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
update.
update(ShareExperiment) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
update.
update(ShareFile) - Method in interface net.sourceforge.seqware.common.business.ShareFileService
update.
update(ShareLane) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
update.
update(ShareProcessing) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
update.
update(ShareSample) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
update.
update(ShareStudy) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
update.
update(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
update.
update(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
update.
update(Registration, Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
update.
update(StudyType) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService
update.
update(WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
update.
update(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
update.
update(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
update.
update(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
update.
update(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
update.
update(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
update.
update(WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
update.
update(WorkflowRun, List<Integer>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
update.
update(Registration, WorkflowRun, List<Integer>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
update.
update(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
update.
update(Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
update.
update(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
update.
update(ExperimentAttribute) - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO
update.
update(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
update.
update(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
update.
update(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO
update.
update(ExperimentLink) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO
update.
update(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO
update.
update(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO
update.
update(FileAttribute) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO
update.
update(File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
update.
update(Registration, File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
update.
update(ExperimentAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate
update.
update(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
update.
update(Registration, Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
update.
update(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate
update.
update(ExperimentLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate
update.
update(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate
update.
update(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate
update.
update(FileAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
update.
update(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
update.
update(Registration, File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
update.
update(Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
update.
update(Registration, Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
update.
update(IUSAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate
update.
update(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
update.
update(Registration, IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
update.
update(IUSLink) - Method in interface net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAO
update.
update(IUSLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate
update.
update(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAO
update.
update(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate
update.
update(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
update.
update(Registration, Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
update.
update(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAO
update.
update(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate
update.
update(ProcessingAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate
update.
update(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
update.
update(Registration, Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
update.
update(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate
update.
update(ProcessingIus) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate
update.
update(ProcessingLanes) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate
update.
update(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate
update.
update(ProcessingSamples) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate
update.
update(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate
update.
update(ProcessingStudies) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate
update.
update(Project) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate
update.
update(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate
update.
update(SampleAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate
update.
update(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
update.
update(Registration, Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
update.
update(SampleLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate
update.
update(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
update.
update(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
update.
update(ShareExperiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
update.
update(ShareFile) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
update.
update(ShareLane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
update.
update(ShareProcessing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
update.
update(ShareSample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
update.
update(ShareStudy) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate
update.
update(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
update.
update(StudyAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate
update.
update(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
update.
update(Registration, Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
update.
update(StudyLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate
update.
update(StudyType) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate
update.
update(WorkflowAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
update.
update(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
update.
update(Registration, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
update.
update(WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
update.
update(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
update.
update(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
update.
update(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
update.
update(WorkflowRunAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
update.
update(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
update.
update(WorkflowRun, List<Integer>) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
update.
update(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
update.
update(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
update.
update(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
update.
update(Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
update.
update(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
update.
update(IUSAttribute) - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO
update.
update(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
update.
update(Registration, IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
update.
update(Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
update.
update(Registration, Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
update.
update(ProcessingAttribute) - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO
update.
update(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
update.
update(Registration, Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
update.
update(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO
update.
update(ProcessingIus) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO
update.
update(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO
update.
update(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO
update.
update(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO
update.
update(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO
update.
update(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO
update.
update(Project) - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO
update.
update(Registration) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO
update.
update(SampleAttribute) - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO
update.
update(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
update.
update(Registration, Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
update.
update(SampleLink) - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO
update.
update(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
update.
update(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
update.
update(ShareExperiment) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO
update.
update(ShareFile) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO
update.
update(ShareLane) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO
update.
update(ShareProcessing) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO
update.
update(ShareSample) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO
update.
update(ShareStudy) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO
update.
update(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
update.
update(StudyAttribute) - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO
update.
update(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
update.
update(Registration, Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
update.
update(StudyLink) - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO
update.
update(StudyType) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO
update.
update(WorkflowAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO
update.
update(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
update.
update(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
update.
update(WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO
update.
update(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO
update.
update(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
update.
update(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
update.
update(WorkflowRunAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO
update.
update(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
update.
update(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
update.
update(WorkflowRun, List<Integer>) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
update.
update(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
update.
update(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
update.
update_processing_event(int, ReturnValue) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
update_processing_event.
update_processing_event(int, ReturnValue) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
update_processing_event.
update_processing_event(int, ReturnValue) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
update_processing_event.
update_processing_event(int, ReturnValue) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
update_processing_event.
update_processing_status(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
update_processing_status.
update_processing_status(int, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
update_processing_status.
update_processing_status(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
update_processing_status.
update_processing_status(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
update_processing_status.
update_processing_workflow_run(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
update_processing_workflow_run.
update_processing_workflow_run(int, int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
update_processing_workflow_run.
update_processing_workflow_run(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
update_processing_workflow_run.
update_processing_workflow_run(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
update_processing_workflow_run.
update_workflow_run(int, String, String, String, String, String, String, String, String, int, int, String, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
update_workflow_run.
update_workflow_run(int, String, String, String, String, String, String, String, String, int, int, String, String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
update_workflow_run.
update_workflow_run(int, String, String, String, String, String, String, String, String, int, int, String, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
update_workflow_run.
update_workflow_run(int, String, String, String, String, String, String, String, String, int, int, String, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
update_workflow_run.
updateACL(ACL) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
updateACL.
updateAnalysisPlugin(AnalysisPlugin) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
updateAnalysisPlugin.
updateAnalysisSet(AnalysisSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
updateAnalysisSet.
updateAndGet(FeatureSet) - Static method in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner
 
updateAttribute(AttributeDto) - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributeResource
updateAttribute.
updateAttribute(AttributeDto) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource
updateAttribute.
updateDetached(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService
updateDetached.
updateDetached(Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
updateDetached.
updateDetached(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService
updateDetached.
updateDetached(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService
updateDetached.
updateDetached(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService
updateDetached.
updateDetached(File) - Method in interface net.sourceforge.seqware.common.business.FileService
updateDetached.
updateDetached(Registration, File) - Method in interface net.sourceforge.seqware.common.business.FileService
updateDetached.
updateDetached(FileType) - Method in interface net.sourceforge.seqware.common.business.FileTypeService
updateDetached.
updateDetached(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl
updateDetached.
updateDetached(Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
updateDetached.
updateDetached(Registration, Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl
updateDetached.
updateDetached(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl
updateDetached.
updateDetached(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl
updateDetached.
updateDetached(File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
updateDetached.
updateDetached(Registration, File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl
updateDetached.
updateDetached(FileType) - Method in class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl
updateDetached.
updateDetached(Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
updateDetached.
updateDetached(Registration, Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl
updateDetached.
updateDetached(IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
updateDetached.
updateDetached(Registration, IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl
updateDetached.
updateDetached(Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
updateDetached.
updateDetached(Registration, Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
updateDetached.
updateDetached(LibrarySelection) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl
updateDetached.
updateDetached(LibrarySource) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl
updateDetached.
updateDetached(LibraryStrategy) - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl
updateDetached.
updateDetached(Organism) - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl
updateDetached.
updateDetached(Platform) - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl
updateDetached.
updateDetached(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
updateDetached.
updateDetached(ProcessingIus) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
updateDetached.
updateDetached(ProcessingLanes) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
updateDetached.
updateDetached(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
updateDetached.
updateDetached(ProcessingSamples) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
updateDetached.
updateDetached(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
updateDetached.
updateDetached(Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
updateDetached.
updateDetached(Registration, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl
updateDetached.
updateDetached(ProcessingStudies) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
updateDetached.
updateDetached(Project) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl
updateDetached.
updateDetached(Registration) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl
updateDetached.
updateDetached(Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
updateDetached.
updateDetached(Registration, Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
updateDetached.
updateDetached(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
updateDetached.
updateDetached(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl
updateDetached.
updateDetached(ShareExperiment) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
updateDetached.
updateDetached(ShareFile) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
updateDetached.
updateDetached(ShareLane) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
updateDetached.
updateDetached(ShareProcessing) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
updateDetached.
updateDetached(ShareSample) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
updateDetached.
updateDetached(ShareStudy) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl
updateDetached.
updateDetached(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl
updateDetached.
updateDetached(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
updateDetached.
updateDetached(Registration, Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
updateDetached.
updateDetached(StudyType) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl
updateDetached.
updateDetached(WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
updateDetached.
updateDetached(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
updateDetached.
updateDetached(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
updateDetached.
updateDetached(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
updateDetached.
updateDetached(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
updateDetached.
updateDetached(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
updateDetached.
updateDetached(WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
updateDetached.
updateDetached(Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
updateDetached.
updateDetached(Registration, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
updateDetached.
updateDetached(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
updateDetached.
updateDetached(Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService
updateDetached.
updateDetached(IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService
updateDetached.
updateDetached(Registration, IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService
updateDetached.
updateDetached(Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService
updateDetached.
updateDetached(Registration, Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService
updateDetached.
updateDetached(LibrarySelection) - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService
updateDetached.
updateDetached(LibrarySource) - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService
updateDetached.
updateDetached(LibraryStrategy) - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService
updateDetached.
updateDetached(Organism) - Method in interface net.sourceforge.seqware.common.business.OrganismService
updateDetached.
updateDetached(Platform) - Method in interface net.sourceforge.seqware.common.business.PlatformService
updateDetached.
updateDetached(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService
updateDetached.
updateDetached(ProcessingIus) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService
updateDetached.
updateDetached(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService
updateDetached.
updateDetached(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService
updateDetached.
updateDetached(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService
updateDetached.
updateDetached(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService
updateDetached.
updateDetached(Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
updateDetached.
updateDetached(Registration, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService
updateDetached.
updateDetached(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService
updateDetached.
updateDetached(Project) - Method in interface net.sourceforge.seqware.common.business.ProjectService
updateDetached.
updateDetached(Registration) - Method in interface net.sourceforge.seqware.common.business.RegistrationService
updateDetached.
updateDetached(Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService
updateDetached.
updateDetached(Registration, Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService
updateDetached.
updateDetached(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
updateDetached.
updateDetached(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService
updateDetached.
updateDetached(ShareExperiment) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService
updateDetached.
updateDetached(ShareFile) - Method in interface net.sourceforge.seqware.common.business.ShareFileService
updateDetached.
updateDetached(ShareLane) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService
updateDetached.
updateDetached(ShareProcessing) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService
updateDetached.
updateDetached(ShareSample) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService
updateDetached.
updateDetached(ShareStudy) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService
updateDetached.
updateDetached(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService
updateDetached.
updateDetached(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
updateDetached.
updateDetached(Registration, Study) - Method in interface net.sourceforge.seqware.common.business.StudyService
updateDetached.
updateDetached(StudyType) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService
updateDetached.
updateDetached(WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
updateDetached.
updateDetached(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService
updateDetached.
updateDetached(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
updateDetached.
updateDetached(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService
updateDetached.
updateDetached(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
updateDetached.
updateDetached(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService
updateDetached.
updateDetached(WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService
updateDetached.
updateDetached(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
updateDetached.
updateDetached(Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService
updateDetached.
updateDetached(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
updateDetached.
updateDetached(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO
updateDetached.
updateDetached(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO
updateDetached.
updateDetached(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO
updateDetached.
updateDetached(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO
updateDetached.
updateDetached(File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
updateDetached.
updateDetached(Registration, File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO
updateDetached.
updateDetached(FileType) - Method in interface net.sourceforge.seqware.common.dao.FileTypeDAO
updateDetached.
updateDetached(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
updateDetached.
updateDetached(Registration, Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate
updateDetached.
updateDetached(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate
updateDetached.
updateDetached(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate
updateDetached.
updateDetached(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate
updateDetached.
updateDetached(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
updateDetached.
updateDetached(Registration, File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate
updateDetached.
updateDetached(FileType) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileTypeDAOHibernate
updateDetached.
updateDetached(Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
updateDetached.
updateDetached(Registration, Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate
updateDetached.
updateDetached(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
updateDetached.
updateDetached(Registration, IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate
updateDetached.
updateDetached(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
updateDetached.
updateDetached(Registration, Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate
updateDetached.
updateDetached(LibrarySelection) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate
updateDetached.
updateDetached(LibrarySource) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate
updateDetached.
updateDetached(LibraryStrategy) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate
updateDetached.
updateDetached(Organism) - Method in class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate
updateDetached.
updateDetached(Platform) - Method in class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate
updateDetached.
updateDetached(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
updateDetached.
updateDetached(Registration, Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate
updateDetached.
updateDetached(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate
updateDetached.
updateDetached(ProcessingIus) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate
updateDetached.
updateDetached(ProcessingLanes) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate
updateDetached.
updateDetached(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate
updateDetached.
updateDetached(ProcessingSamples) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate
updateDetached.
updateDetached(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate
updateDetached.
updateDetached(ProcessingStudies) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate
updateDetached.
updateDetached(Project) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate
updateDetached.
updateDetached(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate
updateDetached.
updateDetached(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
updateDetached.
updateDetached(Registration, Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate
updateDetached.
updateDetached(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
updateDetached.
updateDetached(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate
updateDetached.
updateDetached(ShareExperiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
updateDetached.
updateDetached(ShareFile) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
updateDetached.
updateDetached(ShareLane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
updateDetached.
updateDetached(ShareProcessing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
updateDetached.
updateDetached(ShareSample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
updateDetached.
updateDetached(ShareStudy) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate
updateDetached.
updateDetached(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate
updateDetached.
updateDetached(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
updateDetached.
updateDetached(Registration, Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
updateDetached.
updateDetached(StudyType) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate
updateDetached.
updateDetached(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
updateDetached.
updateDetached(Registration, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
updateDetached.
updateDetached(WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
updateDetached.
updateDetached(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
updateDetached.
updateDetached(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
updateDetached.
updateDetached(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
updateDetached.
updateDetached(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
updateDetached.
updateDetached(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
updateDetached.
updateDetached(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
updateDetached.
updateDetached(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
updateDetached.
updateDetached(Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
updateDetached.
updateDetached(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO
updateDetached.
updateDetached(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
updateDetached.
updateDetached(Registration, IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO
updateDetached.
updateDetached(Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
updateDetached.
updateDetached(Registration, Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO
updateDetached.
updateDetached(LibrarySelection) - Method in interface net.sourceforge.seqware.common.dao.LibrarySelectionDAO
updateDetached.
updateDetached(LibrarySource) - Method in interface net.sourceforge.seqware.common.dao.LibrarySourceDAO
updateDetached.
updateDetached(LibraryStrategy) - Method in interface net.sourceforge.seqware.common.dao.LibraryStrategyDAO
updateDetached.
updateDetached(Organism) - Method in interface net.sourceforge.seqware.common.dao.OrganismDAO
updateDetached.
updateDetached(Platform) - Method in interface net.sourceforge.seqware.common.dao.PlatformDAO
updateDetached.
updateDetached(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
updateDetached.
updateDetached(Registration, Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO
updateDetached.
updateDetached(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO
updateDetached.
updateDetached(ProcessingIus) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO
updateDetached.
updateDetached(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO
updateDetached.
updateDetached(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO
updateDetached.
updateDetached(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO
updateDetached.
updateDetached(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO
updateDetached.
updateDetached(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO
updateDetached.
updateDetached(Project) - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO
updateDetached.
updateDetached(Registration) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO
updateDetached.
updateDetached(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
updateDetached.
updateDetached(Registration, Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO
updateDetached.
updateDetached(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
updateDetached.
updateDetached(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO
updateDetached.
updateDetached(ShareExperiment) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO
updateDetached.
updateDetached(ShareFile) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO
updateDetached.
updateDetached(ShareLane) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO
updateDetached.
updateDetached(ShareProcessing) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO
updateDetached.
updateDetached(ShareSample) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO
updateDetached.
updateDetached(ShareStudy) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO
updateDetached.
updateDetached(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO
updateDetached.
updateDetached(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
updateDetached.
updateDetached(Registration, Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
updateDetached.
updateDetached(StudyType) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO
updateDetached.
updateDetached(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
updateDetached.
updateDetached(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO
updateDetached.
updateDetached(WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO
updateDetached.
updateDetached(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO
updateDetached.
updateDetached(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
updateDetached.
updateDetached(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO
updateDetached.
updateDetached(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
updateDetached.
updateDetached(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO
updateDetached.
updateDetached(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
updateDetached.
updateDetached(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO
updateDetached.
updateElement(String, Atom) - Method in class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
Update an existing element.
updateElementPermissions(String) - Method in class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
Update permissions for a particular element
updateFeature(Feature) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
updateFeature.
updateFeatureSet(FeatureSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
updateFeatureSet.
updateGroup(Group) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
updateGroup.
updateLane(Sample, MultipartFile, MultipartFile, String, String, Registration) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl
updateLane.
updateOwners(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl
updateOwners.
updateOwners(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService
updateOwners.
updateOwners(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate
updateOwners.
updateOwners(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO
updateOwners.
updateReference(Reference) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
updateReference.
updateReferenceSet(ReferenceSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
updateReferenceSet.
updateSelectedIds(HttpServletRequest, String, boolean, List<String>) - Static method in class net.sourceforge.solexatools.util.BulkUtil
updateSelectedIds.
updateTag(Tag) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
updateTag.
updateTagSet(TagSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
updateTagSet.
updateUser(User) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface
updateUser.
updateWorkflow(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
updateWorkflow.
updateWorkflow(int, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface
updateWorkflow.
updateWorkflow(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
updateWorkflow.
updateWorkflow(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
updateWorkflow.
updateWorkflowRun(int, String, String, String, String, String, String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
updateWorkflowRun.
updateWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource
updateWorkflowRun.
upgradeFeatureSGID(Feature) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
upgradeFeatureSGID.
uploadFile(Study, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService
uploadFile.
uploadFile(Experiment, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService
uploadFile.
uploadFile(Sample, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService
uploadFile.
uploadFile(Lane, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService
uploadFile.
uploadFile(IUS, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService
uploadFile.
uploadFile(Processing, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService
uploadFile.
uploadFile(SequencerRun, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService
uploadFile.
uploadFile(Study, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
uploadFile.
uploadFile(Experiment, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
uploadFile.
uploadFile(Sample, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
uploadFile.
uploadFile(Lane, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
uploadFile.
uploadFile(IUS, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
uploadFile.
uploadFile(Processing, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
uploadFile.
uploadFile(SequencerRun, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl
uploadFile.
UploadFile - Class in net.sourceforge.seqware.common.business
UploadFile class.
UploadFile() - Constructor for class net.sourceforge.seqware.common.business.UploadFile
Constructor for UploadFile.
UploadFileController - Class in net.sourceforge.solexatools.webapp.controller
UploadFileController class.
UploadFileController() - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadFileController
Constructor for UploadFileController.
UploadFileController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadFileController
Constructor for UploadFileController.
UploadFileSetupController - Class in net.sourceforge.solexatools.webapp.controller
UploadFileSetupController class.
UploadFileSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
Constructor for UploadFileSetupController.
UploadFileValidator - Class in net.sourceforge.solexatools.validation
UploadFileValidator class.
UploadFileValidator() - Constructor for class net.sourceforge.solexatools.validation.UploadFileValidator
Constructor for UploadFileValidator.
uploadOBO(String) - Method in class com.github.seqware.queryengine.system.rest.resources.PluginResource
Upload a jar file to create a new plugin
uploadOBO(String) - Method in class com.github.seqware.queryengine.system.rest.resources.TagSetResource
Upload an OBO file to create a new tagset for an ontology
uploadRawVCFfile(String, String) - Method in class com.github.seqware.queryengine.system.rest.resources.FeatureSetResource
Upload a raw variant file to create a new featureset
UploadSequence - Class in net.sourceforge.seqware.common.model
 
UploadSequence() - Constructor for class net.sourceforge.seqware.common.model.UploadSequence
Constructor for UploadSequence.
UploadSequenceController - Class in net.sourceforge.solexatools.webapp.controller
UploadSequenceController class.
UploadSequenceController() - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
Constructor for UploadSequenceController.
UploadSequenceController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadSequenceController
Constructor for UploadSequenceController.
UploadSequenceSetupController - Class in net.sourceforge.solexatools.webapp.controller
UploadSequenceSetupController class.
UploadSequenceSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
Constructor for UploadSequenceSetupController.
UploadSequenceValidator - Class in net.sourceforge.solexatools.validation
UploadSequenceValidator class.
UploadSequenceValidator() - Constructor for class net.sourceforge.solexatools.validation.UploadSequenceValidator
Constructor for UploadSequenceValidator.
url - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
url - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
 
url - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
 
url - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK
 
url - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
 
url - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK
 
urlLabel - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
urllink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
 
urllink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
 
urllink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK
 
urllink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK
 
urllink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK
 
urlString - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
 
User - Class in com.github.seqware.queryengine.model
A user of the Generic Feature Store.
User.Builder - Class in com.github.seqware.queryengine.model
 
User.Builder() - Constructor for class com.github.seqware.queryengine.model.User.Builder
 
USER_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
UserIO - Class in com.github.seqware.queryengine.impl.protobufIO
UserIO class.
UserIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.UserIO
 
UserListingResource - Class in com.github.seqware.queryengine.system.rest.resources
 
UserListingResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.UserListingResource
 
UserResource - Class in com.github.seqware.queryengine.system.rest.resources
User resource.
UserResource() - Constructor for class com.github.seqware.queryengine.system.rest.resources.UserResource
 
USERS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
useS3ServerSideEncryption - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
 
UtilIO - Class in com.github.seqware.queryengine.impl.protobufIO
UtilIO class.
UtilIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.UtilIO
 
Utility - Class in com.github.seqware.queryengine.system
Utility procedures for interacting outside the API
Utility() - Constructor for class com.github.seqware.queryengine.system.Utility
 

V

Validate - Class in net.sourceforge.seqware.common.util.filetools.validate
Validate class.
Validate() - Constructor for class net.sourceforge.seqware.common.util.filetools.validate.Validate
 
validate - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
 
validate() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileLinkReportResource
validate.
validate() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileReverseHierarchyDisplayResource
validate.
validate(String) - Method in class net.sourceforge.solexatools.util.HTMLTagValidator
validate.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.FileValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.LaneValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.LoginValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.RegistrationValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.SampleValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunWizardValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.StudyValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.WorkflowParamValidator
Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.WorkflowValidator
Validates the specified Object.
validateBundle(File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle
validateBundle.
validateEmail(String, String, Errors) - Method in class net.sourceforge.solexatools.validation.LoginValidator
Validates an email address.
validateEmailAddressesMatch(String, String, Errors) - Static method in class net.sourceforge.solexatools.validation.RegistrationValidator
Determines if the registration's email address and confirm email address match.
validateEmailNotInUse(String, Errors) - Method in class net.sourceforge.solexatools.validation.RegistrationValidator
validateEmailNotInUse.
validateExists(MultipartFile, String, Errors) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
validateExists.
validateExpectedNumberReads(Experiment, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
validateExpectedNumberReads.
validateExpectedNumberReads(Sample, Errors) - Method in class net.sourceforge.solexatools.validation.SampleValidator
validateExpectedNumberReads.
validateExpectedNumberRuns(Experiment, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
validateExpectedNumberRuns.
validateExpectedNumberRuns(Sample, Errors) - Method in class net.sourceforge.solexatools.validation.SampleValidator
validateExpectedNumberRuns.
validateExtension(String, String, Integer, Errors) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
validateExtension.
validateExtension(MultipartFile, MultipartFile, Integer, Errors) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
validateInvitationCode(String, Errors) - Method in class net.sourceforge.solexatools.validation.RegistrationValidator
validateInvitationCode.
validateLaneCount(SequencerRunWizardDTO, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunWizardValidator
validateLaneCount.
validateName(String, Errors) - Method in class net.sourceforge.solexatools.validation.LaneValidator
Determines if the Lane's email address and confirm email address match.
validateName(String, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
Determines if the experiment's email address and confirm email address match.
validatePasswordsMatch(String, String, Errors) - Static method in class net.sourceforge.solexatools.validation.RegistrationValidator
Determines if the registration's password and confirm password match.
validateProtocol(String, String[], Errors) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
validateProtocol.
validateRefLane(SequencerRun, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
validateRefLane.
validateTitle(Experiment, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentUpdateValidator
 
validateTitle(Experiment, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
Determines if the experiment's email address and confirm email address match.
validateTitle(String, Errors) - Method in class net.sourceforge.solexatools.validation.SampleValidator
Determines if the sample's email address and confirm email address match.
validateTitle(Study, Errors) - Method in class net.sourceforge.solexatools.validation.StudyUpdateValidator
 
validateTitle(Study, Errors) - Method in class net.sourceforge.solexatools.validation.StudyValidator
Determines if the experiment's email address and confirm email address match.
ValidationReportService - Interface in net.sourceforge.seqware.common.business
A collection of reports useful when verifying that data in the SeqWare meta db is correct.
ValidationReportServiceImpl - Class in net.sourceforge.seqware.common.business.impl
 
ValidationReportServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl
 
ValidationReportServiceImpl.ReportEntry - Class in net.sourceforge.seqware.common.business.impl
 
ValidationReportServiceImpl.ReportEntry() - Constructor for class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
 
value - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
 
value - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
 
value - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
 
value - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
 
value - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
 
value - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
 
VALUE_SEPARATOR_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
Constant VALUE_SEPARATOR_PARAM=','
valueOf(String) - Static method in enum com.github.seqware.queryengine.Constants.Term
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
Returns the enum constant of this type with the specified name.
valueOf(int) - Static method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
valueOf(Descriptors.EnumValueDescriptor) - Static method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
 
valueOf(String) - Static method in enum com.github.seqware.queryengine.factory.CreateUpdateManager.State
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.factory.SWQEFactory.Model_Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.factory.SWQEFactory.Serialization_Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.factory.SWQEFactory.Storage_Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.kernel.RPNStack.Operation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.model.Feature.AdditionalAttributeType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.model.Feature.Strand
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.model.QueryInterface.Location
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.model.Tag.ValueType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.plugins.MapperInterface.Counters
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.plugins.PluginInterface.ResultMechanism
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.common.hibernate.FindAllTheFiles.Header
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.deciders.BasicDecider.FILE_STATUS
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.deciders.BasicDecider.PREVIOUS_RUN_STATUS
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.module.ModuleMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.workflow.BasicWorkflow.Job
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Module
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Requirement.Type
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource.SEARCH_TYPE
Returns the enum constant of this type with the specified name.
values() - Static method in enum com.github.seqware.queryengine.Constants.Term
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.factory.CreateUpdateManager.State
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.factory.SWQEFactory.Model_Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.factory.SWQEFactory.Serialization_Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.factory.SWQEFactory.Storage_Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.kernel.RPNStack.Operation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.model.Feature.AdditionalAttributeType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.model.Feature.Strand
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.model.QueryInterface.Location
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.model.Tag.ValueType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.plugins.MapperInterface.Counters
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.plugins.PluginInterface.ResultMechanism
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.common.hibernate.FindAllTheFiles.Header
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.pipeline.deciders.BasicDecider.FILE_STATUS
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.pipeline.deciders.BasicDecider.PREVIOUS_RUN_STATUS
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.pipeline.module.ModuleMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.pipeline.workflow.BasicWorkflow.Job
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Module
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Requirement.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.webservice.resources.tables.FileChildWorkflowRunsResource.SEARCH_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
Variant - Class in net.sourceforge.seqware.queryengine.backend.model
Variant class.
Variant() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.Variant
 
VariantConsequenceByPositionImporter - Class in net.sourceforge.seqware.queryengine.tools.importers
VariantConsequenceByPositionImporter class.
VariantConsequenceByPositionImporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.VariantConsequenceByPositionImporter
 
VariantConsequenceImporter - Class in net.sourceforge.seqware.queryengine.tools.importers
VariantConsequenceImporter class.
VariantConsequenceImporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.VariantConsequenceImporter
 
VariantImporter - Class in net.sourceforge.seqware.queryengine.tools.importers
VariantImporter class.
VariantImporter(int) - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.VariantImporter
Constructor for VariantImporter.
VariantIteratorProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators
VariantIteratorProcessor class.
VariantIteratorProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.VariantIteratorProcessor
 
VariantProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators.processors
VariantProcessor class.
VariantProcessor(String, Store, boolean, boolean, int, int, int, int, int, int) - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Constructor for VariantProcessor.
VariantProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor
Constructor for VariantProcessor.
VariantStatsProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators.processors
VariantStatsProcessor class.
VariantStatsProcessor(String, BerkeleyDBStore, boolean, boolean, int, int, int, int, int, int) - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantStatsProcessor
Constructor for VariantStatsProcessor.
VariantStatsProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantStatsProcessor
Constructor for VariantStatsProcessor.
VariantTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders
VariantTB class.
VariantTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.VariantTB
 
VARIENT - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model
Constant VARIENT=0
VBYTES_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
VCF - Static variable in class com.github.seqware.queryengine.system.exporters.VCFDumper
Constant VCF="VCFVariantImportWorker.VCF"
VCF - Static variable in class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker
Constant VCF="VCF"
VCF_CALLED_BASE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant VCF_CALLED_BASE="call_base"
VCF_CONSENSUS_BASE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant VCF_CONSENSUS_BASE="con_base"
VCF_FILTER - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant VCF_FILTER="filter"
VCF_HETEROZYGOUS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant VCF_HETEROZYGOUS="heterozygous"
VCF_HOMOZYGOUS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant VCF_HOMOZYGOUS="homozygous"
VCF_INFO - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant VCF_INFO="info"
VCF_READ_COUNTS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant VCF_READ_COUNTS="read_count"
VCF_REFERENCE_BASE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant VCF_REFERENCE_BASE="ref_base"
VCF_SECOND_ID - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant VCF_SECOND_ID="id"
VCF_SNV - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Constant VCF_SNV="SNV"
VCFDumper - Class in com.github.seqware.queryengine.system.exporters
This will dump VCF files given a FeatureSet that was originally imported from a VCF file.
VCFDumper(String[]) - Constructor for class com.github.seqware.queryengine.system.exporters.VCFDumper
Constructor for VCFDumper.
VCFDumperPlugin - Class in com.github.seqware.queryengine.plugins.plugins
This plug-in implements a quick and dirty export using Map/Reduce TODO: Copy from HDFS and parse key value file to VCF properly.
VCFDumperPlugin() - Constructor for class com.github.seqware.queryengine.plugins.plugins.VCFDumperPlugin
 
VCFVariantImportWorker - Class in com.github.seqware.queryengine.system.importers.workers
Ported VCFVariantImportWorker now using our Hibernate-like entry.
VCFVariantImportWorker() - Constructor for class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker
Constructor for VCFVariantImportWorker.
VCFVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
VCFVariantImportWorker class.
VCFVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.VCFVariantImportWorker
Constructor for VCFVariantImportWorker.
VDOUBLE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
VenterGenomeVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
VenterGenomeVariantImportWorker class.
VenterGenomeVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.VenterGenomeVariantImportWorker
Constructor for VenterGenomeVariantImportWorker.
verify(String, char[]) - Method in class net.sourceforge.seqware.queryengine.webservice.security.SeqWareVerifier
verifyFile(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
verifyFile.
verifyInput() - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
 
verifyInput() - Method in interface com.github.seqware.queryengine.plugins.PluginInterface
verifyInput.
verifyOutput() - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
 
verifyOutput() - Method in interface com.github.seqware.queryengine.plugins.PluginInterface
verifyOutput.
verifyParameters() - Method in class com.github.seqware.queryengine.plugins.MapReducePlugin
 
verifyParameters() - Method in interface com.github.seqware.queryengine.plugins.PluginInterface
verifyParameters.
version - Variable in class net.sourceforge.seqware.common.module.ReturnValue
 
VERSION - Static variable in class net.sourceforge.seqware.pipeline.module.Module
Constant VERSION="0.7.0"
Versionable<T extends Versionable> - Interface in com.github.seqware.queryengine.model.interfaces
Interface for versioning, versions are automatically generated and iterated when a new entity is derived from a parent entity.
versioningOfElementRequest(String) - Method in class com.github.seqware.queryengine.system.rest.resources.GenericElementResource
Retrieve resources and list their version information.
versionRequest() - Method in class com.github.seqware.queryengine.system.rest.resources.AboutResource
List of versions of the RESTful API this server understands and information about their URIs and what methods they support.
VersionResource - Class in net.sourceforge.seqware.queryengine.webservice.view
VersionResource class.
VersionResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.VersionResource
 
VFLOAT_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
VINTEGER_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
VLONG_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
VSGIDREF_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
VSTRING_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 

W

WAIT - Static variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
 
waitAndGetReturn(Process) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools
Wait on a process to finish, then parse information into return value
warn(Object) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.warn(Object).
warn(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log
See Category.warn(Object,Throwable).
watchModuleRun(ProceedingJoinPoint) - Method in class net.sourceforge.seqware.pipeline.runner.LogAspect
watchModuleRun.
watchModuleRun2(ProceedingJoinPoint) - Method in class net.sourceforge.seqware.pipeline.runner.RedirectAspect
watchModuleRun2.
watchRunner(ProceedingJoinPoint) - Method in class net.sourceforge.seqware.pipeline.runner.LogAspect
watchRunner.
watchWorkflow(String, String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
This method allows you to monitor a running Pegasus workflow using a statusCmd (typically something like "pegasus-status -l dir" and, if something goes wrong, it will return false.
watchWorkflow(String, String, int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
This method allows you to monitor a running Pegasus workflow using a statusCmd (typically something like "pegasus-status -l dir" and, if something goes wrong, it will return a ReturnValue with exit status of ReturnValue.FAILURE, ReturnValue.PROCESSING if still running, and ReturnValue.SUCCESS if finished OK.
WatsonGenomeVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
WatsonGenomeVariantImportWorker class.
WatsonGenomeVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.WatsonGenomeVariantImportWorker
Constructor for WatsonGenomeVariantImportWorker.
wfCount(Sample) - Static method in class net.sourceforge.solexatools.util.TagUtils
Returns count of the Sample related Workflow Runs.
wfrAccession - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
wfrAccession - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
wfrAncesstor - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob
 
wfrAncesstor - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
 
WHITESPACE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
Constant WHITESPACE=25
WHITESPACE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
Constant WHITESPACE=25
whoAmI() - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
This tool uses the 'whoami' command to find the current user versus the user.name method.
WIGExporter - Class in net.sourceforge.seqware.queryengine.tools.exporters
WIGExporter class.
WIGExporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.exporters.WIGExporter
 
WORKER_CHAR_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter
Constant WORKER_CHAR_PARAM='w'
workerName - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
 
Workflow - Class in net.sourceforge.seqware.common.model
Workflow class.
Workflow() - Constructor for class net.sourceforge.seqware.common.model.Workflow
Constructor for Workflow.
Workflow - Class in net.sourceforge.seqware.pipeline.workflow
FIXME: This Workflow object should have much of the implementation move to the common package, see WorkflowTools
Workflow(Metadata, Map<String, String>) - Constructor for class net.sourceforge.seqware.pipeline.workflow.Workflow
Constructor for Workflow.
Workflow - Class in net.sourceforge.seqware.pipeline.workflowV2.model
 
Workflow() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
 
WORKFLOW_CLASS - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility
 
WORKFLOW_ENGINE - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility
 
WORKFLOW_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant WORKFLOW_NAME="Header.WORKFLOW_NAME.getTitle()"
WORKFLOW_RUN_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant WORKFLOW_RUN_NAME="Header.WORKFLOW_RUN_NAME.getTitle()"
WORKFLOW_RUN_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant
Constant WORKFLOW_RUN_PREFIX="wfr_"
WORKFLOW_RUN_STATUS - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant WORKFLOW_RUN_STATUS="Header.WORKFLOW_RUN_STATUS.getTitle()"
WORKFLOW_RUN_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant WORKFLOW_RUN_SWA="Header.WORKFLOW_RUN_SWA.getTitle()"
WORKFLOW_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant WORKFLOW_SWA="Header.WORKFLOW_SWA.getTitle()"
WORKFLOW_TYPE - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility
 
WORKFLOW_VERSION - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
Constant WORKFLOW_VERSION="Header.WORKFLOW_VERSION.getTitle()"
WorkflowApp - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object
 
WorkflowApp(AbstractWorkflowDataModel, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.WorkflowApp
 
WorkflowAttribute - Class in net.sourceforge.seqware.common.model
 
WorkflowAttribute() - Constructor for class net.sourceforge.seqware.common.model.WorkflowAttribute
 
WorkflowAttributeDAO - Interface in net.sourceforge.seqware.common.dao
WorkflowAttributeDAO interface.
WorkflowAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
WorkflowAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
 
WorkflowClassFinder - Class in net.sourceforge.seqware.pipeline.workflowV2
WorkflowClassFinder class.
WorkflowClassFinder() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.WorkflowClassFinder
Constructor for WorkflowClassFinder.
WorkflowController - Class in net.sourceforge.solexatools.webapp.controller
WorkflowController class.
WorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowController
Constructor for WorkflowController.
WorkflowController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowController
Constructor for WorkflowController.
WorkflowDAO - Interface in net.sourceforge.seqware.common.dao
WorkflowDAO interface.
WorkflowDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
WorkflowDAOHibernate class.
WorkflowDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate
Constructor for WorkflowDAOHibernate.
WorkflowDataModelFactory - Class in net.sourceforge.seqware.pipeline.workflowV2
a utils class for creating the AbstractWorkflowDataModel, by reading the metadata.xml file, will load a Java based objectModel or XML based ObjectModel
WorkflowDataModelFactory(OptionSet, Map<String, String>, String[], Metadata) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.WorkflowDataModelFactory
 
WorkflowEngine - Interface in net.sourceforge.seqware.pipeline.workflowV2
WorkflowEngine interface.
WorkflowExecutable - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object
 
WorkflowExecutable() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
 
WorkflowExecutableUtils - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus
a util class to generate Java, Perl, and DirManager for dax
WorkflowExecutableUtils() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.WorkflowExecutableUtils
 
WorkflowIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
WorkflowIDResource class.
WorkflowIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource
Constructor for WorkflowIDResource.
WorkflowInfo - Class in net.sourceforge.seqware.common.util.workflowtools
WorkflowInfo class.
WorkflowInfo() - Constructor for class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
 
WorkflowLauncher - Class in net.sourceforge.seqware.pipeline.plugins
 
WorkflowLauncher() - Constructor for class net.sourceforge.seqware.pipeline.plugins.WorkflowLauncher
 
WorkflowList - Class in net.sourceforge.seqware.common.model.lists
WorkflowList class.
WorkflowList() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowList
Constructor for WorkflowList.
WorkflowListSetupController - Class in net.sourceforge.solexatools.webapp.controller
RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
WorkflowListSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController
Constructor for WorkflowListSetupController.
WorkflowManager - Class in net.sourceforge.seqware.common.util.workflowtools
WorkflowManager class.
WorkflowManager() - Constructor for class net.sourceforge.seqware.common.util.workflowtools.WorkflowManager
 
WorkflowParam - Class in net.sourceforge.seqware.common.model
WorkflowParam class.
WorkflowParam() - Constructor for class net.sourceforge.seqware.common.model.WorkflowParam
Constructor for WorkflowParam.
WorkflowParamController - Class in net.sourceforge.solexatools.webapp.controller
WorkflowParamController class.
WorkflowParamController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
Constructor for WorkflowParamController.
WorkflowParamController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamController
Constructor for WorkflowParamController.
WorkflowParamDAO - Interface in net.sourceforge.seqware.common.dao
WorkflowParamDAO interface.
WorkflowParamDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
WorkflowParamDAOHibernate class.
WorkflowParamDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate
Constructor for WorkflowParamDAOHibernate.
WorkflowParamIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
WorkflowParamIDResource class.
WorkflowParamIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamIDResource
Constructor for WorkflowParamIDResource.
WorkflowParamList - Class in net.sourceforge.seqware.common.model.lists
WorkflowParamList class.
WorkflowParamList() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowParamList
Constructor for WorkflowParamList.
WorkflowParamListController - Class in net.sourceforge.solexatools.webapp.controller
WorkflowParamListController class.
WorkflowParamListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController
Constructor for WorkflowParamListController.
WorkflowParamResource - Class in net.sourceforge.seqware.webservice.resources.tables
WorkflowParamResource class.
WorkflowParamResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamResource
Constructor for WorkflowParamResource.
WorkflowParamService - Interface in net.sourceforge.seqware.common.business
WorkflowParamService interface.
WorkflowParamServiceImpl - Class in net.sourceforge.seqware.common.business.impl
WorkflowParamServiceImpl class.
WorkflowParamServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl
Constructor for WorkflowParamServiceImpl.
WorkflowParamSetupController - Class in net.sourceforge.solexatools.webapp.controller
WorkflowParamSetupController class.
WorkflowParamSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController
Constructor for WorkflowParamSetupController.
WorkflowParamValidator - Class in net.sourceforge.solexatools.validation
WorkflowParamValidator class.
WorkflowParamValidator() - Constructor for class net.sourceforge.solexatools.validation.WorkflowParamValidator
Constructor for WorkflowParamValidator.
WorkflowParamValue - Class in net.sourceforge.seqware.common.model
WorkflowParamValue class.
WorkflowParamValue() - Constructor for class net.sourceforge.seqware.common.model.WorkflowParamValue
Constructor for WorkflowParamValue.
WorkflowParamValueController - Class in net.sourceforge.solexatools.webapp.controller
WorkflowParamValueController class.
WorkflowParamValueController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
Constructor for WorkflowParamValueController.
WorkflowParamValueController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController
Constructor for WorkflowParamValueController.
WorkflowParamValueDAO - Interface in net.sourceforge.seqware.common.dao
WorkflowParamValueDAO interface.
WorkflowParamValueDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
WorkflowParamValueDAOHibernate class.
WorkflowParamValueDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate
Constructor for WorkflowParamValueDAOHibernate.
WorkflowParamValueIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
WorkflowParamValueIDResource class.
WorkflowParamValueIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueIDResource
Constructor for WorkflowParamValueIDResource.
WorkflowParamValueList - Class in net.sourceforge.seqware.common.model.lists
WorkflowParamValueList class.
WorkflowParamValueList() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList
Constructor for WorkflowParamValueList.
WorkflowParamValueResource - Class in net.sourceforge.seqware.webservice.resources.tables
WorkflowParamValueResource class.
WorkflowParamValueResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueResource
Constructor for WorkflowParamValueResource.
WorkflowParamValueService - Interface in net.sourceforge.seqware.common.business
WorkflowParamValueService interface.
WorkflowParamValueServiceImpl - Class in net.sourceforge.seqware.common.business.impl
WorkflowParamValueServiceImpl class.
WorkflowParamValueServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl
Constructor for WorkflowParamValueServiceImpl.
WorkflowParamValueSetupController - Class in net.sourceforge.solexatools.webapp.controller
WorkflowParamValueSetupController class.
WorkflowParamValueSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
Constructor for WorkflowParamValueSetupController.
WorkflowPlugin - Class in net.sourceforge.seqware.pipeline.plugin
TODO: validate at all the option below (especially link-parent-to-workflow-run) actually work!
WorkflowPlugin() - Constructor for class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
 
WorkflowReport - Class in net.sourceforge.seqware.common.hibernate
WorkflowReport class.
WorkflowReport() - Constructor for class net.sourceforge.seqware.common.hibernate.WorkflowReport
 
WorkflowReportResource - Class in net.sourceforge.seqware.webservice.resources.queries
WorkflowReportResource class.
WorkflowReportResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowReportResource
Constructor for WorkflowReportResource.
WorkflowResource - Class in net.sourceforge.seqware.queryengine.webservice.view
WorkflowResource class.
WorkflowResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.WorkflowResource
 
WorkflowResource - Class in net.sourceforge.seqware.webservice.resources.tables
WorkflowResource class.
WorkflowResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowResource
Constructor for WorkflowResource.
WorkflowRun - Class in net.sourceforge.seqware.common.model
WorkflowRun class.
WorkflowRun() - Constructor for class net.sourceforge.seqware.common.model.WorkflowRun
Constructor for WorkflowRun.
WorkflowRunAttribute - Class in net.sourceforge.seqware.common.model
 
WorkflowRunAttribute() - Constructor for class net.sourceforge.seqware.common.model.WorkflowRunAttribute
 
WorkflowRunAttributeDAO - Interface in net.sourceforge.seqware.common.dao
WorkflowRunAttributeDAO interface.
WorkflowRunAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
 
WorkflowRunAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
 
WorkflowRunController - Class in net.sourceforge.solexatools.webapp.controller
WorkflowRunController class.
WorkflowRunController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
Constructor for WorkflowRunController.
WorkflowRunController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowRunController
Constructor for WorkflowRunController.
WorkflowRunDAO - Interface in net.sourceforge.seqware.common.dao
WorkflowRunDAO interface.
WorkflowRunDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
WorkflowRunDAOHibernate class.
WorkflowRunDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate
Constructor for WorkflowRunDAOHibernate.
WorkflowRunHtmlUtil - Class in net.sourceforge.solexatools.util
WorkflowRunHtmlUtil class.
WorkflowRunHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
 
WorkflowRunIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries
WorkflowRunIdFilesResource class.
WorkflowRunIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIdFilesResource
Constructor for WorkflowRunIdFilesResource.
WorkflowRunIDProcessingsResource - Class in net.sourceforge.seqware.webservice.resources.queries
WorkflowRunIDProcessingsResource class.
WorkflowRunIDProcessingsResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDProcessingsResource
Constructor for WorkflowRunIDProcessingsResource.
WorkflowRunIDResource - Class in net.sourceforge.seqware.webservice.resources.tables
WorkflowRunIDResource class.
WorkflowRunIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource
Constructor for WorkflowRunIDResource.
WorkflowRunIDsFilter - Class in net.sourceforge.seqware.webservice.resources.filters
We presume there is either a runId or a testId, not both.
WorkflowRunIDsFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunIDsFilter
 
WorkflowRunIDWorkflowResource - Class in net.sourceforge.seqware.webservice.resources.queries
WorkflowRunIDWorkflowResource class.
WorkflowRunIDWorkflowResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDWorkflowResource
Constructor for WorkflowRunIDWorkflowResource.
WorkflowRunList - Class in net.sourceforge.seqware.common.model.lists
WorkflowRunList class.
WorkflowRunList() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowRunList
Constructor for WorkflowRunList.
WorkflowRunList2 - Class in net.sourceforge.seqware.common.model.lists
WorkflowRunList2 class.
WorkflowRunList2() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowRunList2
Constructor for WorkflowRunList2.
WorkflowRunParam - Class in net.sourceforge.seqware.common.model
WorkflowRunParam class.
WorkflowRunParam() - Constructor for class net.sourceforge.seqware.common.model.WorkflowRunParam
Constructor for WorkflowRunParam.
WorkflowRunParamDAO - Interface in net.sourceforge.seqware.common.dao
WorkflowRunParamDAO interface.
WorkflowRunParamDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
WorkflowRunParamDAOHibernate class.
WorkflowRunParamDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate
Constructor for WorkflowRunParamDAOHibernate.
WorkflowRunParamService - Interface in net.sourceforge.seqware.common.business
WorkflowRunParamService interface.
WorkflowRunParamServiceImpl - Class in net.sourceforge.seqware.common.business.impl
WorkflowRunParamServiceImpl class.
WorkflowRunParamServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl
Constructor for WorkflowRunParamServiceImpl.
WorkflowRunReport - Class in net.sourceforge.seqware.common.hibernate
Reports on workflow run metadata, returning either all workflow runs, all runs of a particular workflow, or a specific workflow run.
WorkflowRunReport() - Constructor for class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
 
WorkflowRunReporter - Class in net.sourceforge.seqware.pipeline.plugins
WorkflowRunReporter class.
WorkflowRunReporter() - Constructor for class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter
Constructor for WorkflowRunReporter.
WorkflowRunReportResource - Class in net.sourceforge.seqware.webservice.resources.queries
WorkflowRunReportResource class.
WorkflowRunReportResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource
Constructor for WorkflowRunReportResource.
WorkflowRunReportRow - Class in net.sourceforge.seqware.common.hibernate.reports
Contains the workflow's Processing events, the parent Processings, the input files, the output files, the identity and library samples, as well as the total running time.
WorkflowRunReportRow() - Constructor for class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
 
WorkflowRunResource - Class in net.sourceforge.seqware.webservice.resources.tables
WorkflowRunResource class.
WorkflowRunResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource
Constructor for WorkflowRunResource.
WorkflowRunService - Interface in net.sourceforge.seqware.common.business
WorkflowRunService interface.
WorkflowRunServiceImpl - Class in net.sourceforge.seqware.common.business.impl
WorkflowRunServiceImpl class.
WorkflowRunServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl
Constructor for WorkflowRunServiceImpl.
WorkflowRunSetupController - Class in net.sourceforge.solexatools.webapp.controller
WorkflowRunSetupController class.
WorkflowRunSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController
 
WorkflowRunsFilter - Class in net.sourceforge.seqware.webservice.resources.filters
We presume there is either a runId or a testId, not both.
WorkflowRunsFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter
 
WorkflowRunStatusResource - Class in net.sourceforge.seqware.queryengine.webservice.view
WorkflowRunStatusResource class.
WorkflowRunStatusResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.WorkflowRunStatusResource
 
WorkflowRuntimeResource - Class in net.sourceforge.seqware.webservice.resources.queries
WorkflowRuntimeResource class.
WorkflowRuntimeResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRuntimeResource
Constructor for WorkflowRuntimeResource.
WorkflowService - Interface in net.sourceforge.seqware.common.business
WorkflowService interface.
workflowService - Variable in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController
 
WorkflowServiceImpl - Class in net.sourceforge.seqware.common.business.impl
WorkflowServiceImpl class.
WorkflowServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl
Constructor for WorkflowServiceImpl.
WorkflowSetupController - Class in net.sourceforge.solexatools.webapp.controller
WorkflowSetupController class.
WorkflowSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController
Constructor for WorkflowSetupController.
WorkflowStatusChecker - Class in net.sourceforge.seqware.pipeline.plugins
This plugin lets you monitor the status of running workflows and updates the metadata object with their status.
WorkflowStatusChecker() - Constructor for class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker
Constructor for WorkflowStatusChecker.
WorkflowTools - Class in net.sourceforge.seqware.common.util.workflowtools
This class provides methods for dealing with Pegasus workflow log directories for example watching a directory to detect when a workflow has failed or finished.
WorkflowTools() - Constructor for class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
 
workflowTools - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
 
WorkflowV2Utility - Class in net.sourceforge.seqware.pipeline.workflowV2
Utility methods that have been refactored out.
WorkflowV2Utility() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.WorkflowV2Utility
 
WorkflowValidator - Class in net.sourceforge.solexatools.validation
WorkflowValidator class.
WorkflowValidator() - Constructor for class net.sourceforge.solexatools.validation.WorkflowValidator
Constructor for WorkflowValidator.
WorkflowXmlParser - Class in net.sourceforge.seqware.pipeline.workflowV2
 
WorkflowXmlParser() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.WorkflowXmlParser
 
wrapup() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
to be Overridden by the workflow author
write(KEYOUT, VALUEOUT) - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner.PluginRunnerMapper
 
write(KEYOUT, VALUEOUT) - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRHBasePluginRunner.PluginRunnerReducer
 
write(Object, Object) - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryPluginRunner
 
write(KEYOUT, VALUEOUT) - Method in interface com.github.seqware.queryengine.plugins.MapperInterface
 
write(REDUCEKEYOUT, REDUCEVALUEOUT) - Method in interface com.github.seqware.queryengine.plugins.ReducerInterface
 
write(Kryo, Output) - Method in class com.github.seqware.queryengine.util.FSGID
write(Kryo, Output) - Method in class com.github.seqware.queryengine.util.SGID
writeKeyValueFile(File, Map<String, String>) - Static method in class com.github.seqware.queryengine.system.Utility
Write to output file a tab separated key value file represented by map
writer() - Method in class net.sourceforge.seqware.common.util.runtools.ConsoleAdapter
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.PluginRunPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
 
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
 
WS_PASS - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
 
WS_URL - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
 
WS_USER - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
 

X

XmlizeFileSet - Class in net.sourceforge.seqware.common.model.adapters
XmlizeFileSet class.
XmlizeFileSet() - Constructor for class net.sourceforge.seqware.common.model.adapters.XmlizeFileSet
 
XmlizeIUSSortedSet - Class in net.sourceforge.seqware.common.model.adapters
XmlizeIUSSortedSet class.
XmlizeIUSSortedSet() - Constructor for class net.sourceforge.seqware.common.model.adapters.XmlizeIUSSortedSet
 
XmlizeLaneSortedSet - Class in net.sourceforge.seqware.common.model.adapters
XmlizeLaneSortedSet class.
XmlizeLaneSortedSet() - Constructor for class net.sourceforge.seqware.common.model.adapters.XmlizeLaneSortedSet
 
XmlizeXML - Class in net.sourceforge.seqware.common.model.adapters
XmlizeXML class.
XmlizeXML() - Constructor for class net.sourceforge.seqware.common.model.adapters.XmlizeXML
 
XmlTools - Class in net.sourceforge.seqware.common.util.xmltools
XmlTools class.
XmlTools() - Constructor for class net.sourceforge.seqware.common.util.xmltools.XmlTools
 
XmlWorkflowDataModel - Class in net.sourceforge.seqware.pipeline.workflowV2.model
 
XmlWorkflowDataModel() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.XmlWorkflowDataModel
 
xreflink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
 
XSI - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Adag
 

Y

YanHuangGenomeVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers
YanHuangGenomeVariantImportWorker class.
YanHuangGenomeVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.YanHuangGenomeVariantImportWorker
Constructor for YanHuangGenomeVariantImportWorker.

Z

Zip - Class in net.sourceforge.seqware.pipeline.tools
Zip class.
Zip() - Constructor for class net.sourceforge.seqware.pipeline.tools.Zip
 
zipDirectoryRecursive(File, File, String, boolean, boolean) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
zipDirectoryRecursive.
zipDirectoryRecursiveOld(File, File, String, boolean, boolean) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
zipDirectoryRecursiveOld.
ZipFileUtil - Class in net.sourceforge.solexatools.util
ZipFileUtil class.
ZipFileUtil() - Constructor for class net.sourceforge.solexatools.util.ZipFileUtil
 
zipListFileRecursiveOld(List<File>, File, String, String, boolean) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools
zipListFileRecursiveOld.
zygosity - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
 

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